<PAGE>   1


                                  UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                                    FORM 10-Q

 (MARK ONE)

  X               QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
 ---              SECURITIES EXCHANGE ACT OF 1934
                  FOR THE QUARTERLY PERIOD ENDED MARCH 31, 1999
                                            OR
 ---              TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF
                  THE SECURITIES EXCHANGE ACT OF 1934

                         COMMISSION FILE NUMBER 1-11871

                      COMMODORE APPLIED TECHNOLOGIES, INC.
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)


                    DELAWARE                                 11-3312952
        (STATE OR OTHER JURISDICTION OF                   (I.R.S. EMPLOYER
         INCORPORATION OR ORGANIZATION)                 IDENTIFICATION NO.)


              150 EAST 58TH STREET
               NEW YORK, NEW YORK                              10155
    (ADDRESS OF PRINCIPAL EXECUTIVE OFFICE)                  (ZIP CODE)


REGISTRANT'S TELEPHONE NUMBER, INCLUDING AREA CODE:   (212) 308-5800


     Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding 12 months (or for such shorter period that the
registrant was required to file such reports), and (2) has been subject to such
filing requirements for the past 90 days. Yes X No   .
                                             ---  ---

     The number of shares the common stock outstanding at May 5, 1999 was
23,702,263.


<PAGE>   2


                      COMMODORE APPLIED TECHNOLOGIES, INC.

                                    FORM 10-Q

                                      INDEX


<TABLE>
<CAPTION>
                                                                                              PAGE NO.
<S>           <C>                                                                             <C>
PART I   FINANCIAL INFORMATION....................................................................1

Item 1.       Financial Statements (Unaudited)

              Condensed Consolidated Balance Sheet -
                      March 31, 1999 and December 31, 1998........................................1

              Condensed Consolidated Statement of Operations -
                      Three months ended March 31, 1999 and
                      March 31, 1998..............................................................3

              Condensed Consolidated Statement of Cash Flows Three months ended
                      March 31, 1999 and
                      March 31, 1998..............................................................4

              Notes to Condensed Consolidated Financial Statements................................5

Item 2.       Management's Discussion and Analysis of Financial
                      Condition and Results of Operations.........................................9

PART II  OTHER INFORMATION.......................................................................15

SIGNATURES    ...................................................................................16
</TABLE>

                                       i

<PAGE>   3




                         PART I - FINANCIAL INFORMATION

ITEM 1:  FINANCIAL STATEMENTS


              COMMODORE APPLIED TECHNOLOGIES, INC. AND SUBSIDIARIES

                      CONDENSED CONSOLIDATED BALANCE SHEET
                  (DOLLARS IN THOUSANDS, EXCEPT PER SHARE DATA)


<TABLE>
<CAPTION>
                                                        MARCH 31,   DECEMBER 31,
                               ASSETS                    1999          1998
                                                        ---------   ------------
<S>                                                     <C>         <C>         
                                                        (unaudited)
Current Assets:
         Cash and cash equivalents                      $     562   $      1,798
         Accounts receivable, net                           2,738          3,142
         Notes and advances to related parties                116            130
         Prepaid assets and other current receivables         287            271
                                                        ---------   ------------
                  Total Current Assets                      3,703          5,341

Property and equipment, net                                 2,374          2,202
Other assets
         Patents and completed technology, net of
            accumulated amortization of $379 and
            $349, respectively                                946            977
         Goodwill, net of accumulated amortization
            of $639 and $575, respectively                  7,033          7,097
                                                        ---------   ------------
                    Total Assets                        $  14,056   $     15,617
                                                        =========   ============
</TABLE>


            See notes to condensed consolidated financial statements.

                                       1
<PAGE>   4



              COMMODORE APPLIED TECHNOLOGIES, INC. AND SUBSIDIARIES

                      CONDENSED CONSOLIDATED BALANCE SHEET
                  (DOLLARS IN THOUSANDS, EXCEPT PER SHARE DATA)

<TABLE>
<CAPTION>
                                                        MARCH 31,   DECEMBER 31,
                      LIABILITIES AND                     1999          1998
                    STOCKHOLDERS' EQUITY                ---------   ------------
<S>                                                     <C>         <C>         
                                                        (unaudited)
Current Liabilities:
         Accounts payable                               $     701   $        975
         Current portion of long term debt                      4              5 
         Line of credit                                       388            361
         Other accrued liabilities                          1,754          2,183
                                                        ---------   ------------
                  Total Current Liabilities                 2,847          3,524

Notes payable to related parties                              181            185
                                                        ---------   ------------
                   Total Liabilities                        3,028          3,709

Commitments and contingencies                                  --             --

Stockholders' Equity
         Convertible Preferred Stock, Series B, C & D
           Par value $0.001 per share,
           6% non-cumulative dividends,
           65,000 shares authorized,
           51,489 shares issued and outstanding                --             --
         Common Stock, par value $0.001 per share,
           75,000,000 shares authorized,
           23,702,263 issued and outstanding                   24             24
         Additional paid-in capital                        43,382         43,382
         Accumulated deficit                              (36,325)       (35,445)
         Accumulated Other Comprehensive Income             3,947          3,947
                                                        ---------    -----------
                  Total Stockholders' Equity               11,028         11,908
                                                        ---------    -----------
         Total Liabilities and Stockholders' Equity     $  14,056    $    15,617
                                                        =========    ===========
</TABLE>



            See notes to condensed consolidated financial statements.



                                       2
<PAGE>   5

             COMMODORE APPLIED TECHNOLOGIES, INC. AND SUBSIDIARIES

                 CONDENSED CONSOLIDATED STATEMENT OF OPERATIONS
            (UNAUDITED - DOLLARS IN THOUSANDS, EXCEPT PER SHARE DATA)



<TABLE>
<CAPTION>
                                                               THREE MONTHS ENDED
                                                              MARCH 31,   MARCH 31,
                                                                1999        1998
                                                              ---------   ---------
<S>                                                           <C>         <C>     
Contract revenues                                              $  3,345    $  4,214
Costs and expenses:
         Cost of sales                                            3,004       3,807
         Research and development                                   285         836
         General and administrative                                 751       2,142
         Depreciation and amortization                              187         295
                                                               --------    --------
                  Total costs and expenses                        4,227       7,080
                                                               --------    --------
Loss from operations                                               (882)     (2,866)
                                                               --------    --------
Other income (expense):
         Interest income                                             17         163
         Interest expense                                           (15)       (244)
                                                               --------    --------
                  Net other income (expense)                          2         (81)
                                                               --------    --------
Loss before income taxes and affiliate losses                      (880)     (2,947)
         Income taxes                                                --          --
                                                               --------    --------
Loss before affiliate losses                                       (880)     (2,947)
         Equity in losses of unconsolidated subsidiaries             --        (448)
                                                               --------    --------
         Net loss                                              $   (880)   $ (3,395)
                                                               ========    ========
         Loss per share                                        $   (.04)   $   (.15)
                                                               ========    ========
Number of weighted average shares outstanding (in thousands)     23,702      22,950
                                                               ========    ========
</TABLE>


            See notes to condensed consolidated financial statements.


                                       3
<PAGE>   6


              COMMODORE APPLIED TECHNOLOGIES, INC. AND SUBSIDIARIES

                 CONDENSED CONSOLIDATED STATEMENT OF CASH FLOWS
            (UNAUDITED - DOLLARS IN THOUSANDS, EXCEPT PER SHARE DATA)

<TABLE>
<CAPTION>
                                                                      THREE MONTHS ENDED
                                                                     MARCH 31,   MARCH 31,
                                                                       1999        1998
                                                                     ---------   ---------
<S>                                                                  <C>         <C>     

CASH FLOWS FROM OPERATING ACTIVITIES:
     Net loss                                                        $   (880)   $ (3,395)
     Adjustments to reconcile net loss to net cash used in
     operating activities:
         Depreciation and amortization                                    187         294
         Undistributed losses of unconsolidated subsidiary                 --         448
         Non-cash interest expense                                         --          89
         Changes in assets and liabilities, net of acquisitions:
                Accounts receivable                                       404        (731)
                Prepaid assets                                            (16)         34
                Inventory                                                  --        (266)
                Other assets                                               --           5
                Accounts payable                                         (274)         97
                Payables to related parties                                (5)        (55)
                Other liabilities                                        (429)       (624)
                                                                     --------    --------
                  Net cash provided/(used) in operating activities     (1,013)     (4,104)

CASH FLOWS FROM INVESTING ACTIVITIES:
      Purchase of equipment                                              (265)       (325)
      Acquisition of patents                                               --         (37)
      Advances to related parties                                          15       1,606
      Decrease (increase) in restricted cash                               --          30
      Other investments                                                    --        (431)
      Other receivables                                                    --          14
                                                                     --------    --------
                  Net cash provided/(used) in investing activities       (250)        857

CASH FLOWS FROM FINANCING ACTIVITIES:
      Net borrowing from principal stockholder                             --       3,450
      Increase in (repayment of) line of credit                            27         149
      Proceeds from subsidiary's sale of stock                             --          25
      Decrease in notes and loans payable                                  --         (14)
      Preferred stock dividend paid                                        --         (14)
      Preferred stock dividend paid by subsidiary                          --        (150)
                                                                     --------    --------
                  Net cash provided/(used) in financing activities         27       3,446
Increase (decrease) in cash                                            (1,236)        199
Cash, beginning of period                                               1,798      13,151
                                                                     --------    --------
Cash, end of period                                                  $    562    $ 13,350
                                                                     ========    ========
</TABLE>

            See notes to condensed consolidated financial statements.


                                       4
<PAGE>   7


              COMMODORE APPLIED TECHNOLOGIES, INC. AND SUBSIDIARIES

        NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED)

                                 MARCH 31, 1999

Note A - Basis of Presentation

         The accompanying unaudited condensed consolidated financial statements
for Commodore Applied Technologies, Inc. and subsidiaries (the "Company" or
"Applied") have been prepared in accordance with generally accepted accounting
principles for interim financial information and with the instructions to Form
10-Q and Article 10 of Regulation S-X. The financial statement information was
derived from unaudited financial statements unless indicated otherwise.
Accordingly, they do not include all of the information and footnotes required
by generally accepted accounting principles for complete financial statements.

         In the opinion of management, all adjustments (consisting of normal
recurring accruals) considered necessary for a fair presentation have been
included. Operating results for the three month period ended March 31, 1999 are
not necessarily indicative of the results that may be expected for the year
ending December 31, 1999.

         The accompanying unaudited condensed consolidated financial statements
should be read in conjunction with the Company's audited financial statements
included in the Company's annual report on form 10-K for the year ended December
31, 1998.

         Certain prior-year amounts have been reclassified to conform to the
current year presentation.

         The accompanying financial statements have been prepared under the
assumption that Applied will continue as a going concern. Such assumption
contemplates the realization of assets and the satisfaction of liabilities in
the normal course of business. For the years ended December 31, 1998, 1997, and
1996, Applied incurred losses exclusive of their gains on the sale of an
affiliate and extraordinary item of $13,353,000, $15,694,000 and $5,643,000,
respectively. Applied has also experienced net cash outflows from operating
activities of $9,155,000, $8,220,000 and $7,159,000 for the years ended December
31, 1998, 1997 and 1996, respectively. Presently, Applied does not have
sufficient cash resources to meet its requirements in 1999. The financial
statements do not include any adjustments that might be necessary should Applied
be unable to continue as a going concern. Applied's continuation as a going
concern is dependent upon its ability to generate sufficient cash flow to meet
its obligations on a timely basis, to obtain additional financing as may be
required, and ultimately to attain profitability. Potential sources of cash
include new contracts, external debt, the sale of new shares of company stock or
alternative methods such as mergers or sale transactions. No assurances can be
given, however, that Applied will be able to obtain any of these potential
sources of cash.

         Anticipated losses on contracts are provided for by a charge to income
during the period such losses are identified. Changes in job performance, job
conditions, estimated profitability (including those arising from contract
penalty provisions) and final contract settlements may result in revisions to
cost and income and are recognized in the period in which the revisions are
determined. Allowances for anticipated losses totaled $132,000 at December 31,
1998 and $118,000 at March 31, 1999.

         The consolidated financial statements include the accounts of the
Company and its majority-owned subsidiaries. All significant intercompany
balances and transactions have been eliminated. The investment in
Teledyne-Commodore, LLC, a 50% owned joint venture with Teledyne Environmental,
Inc., has been accounted for under the equity method as the Company does not
have a controlling interest in the venture. This investment is carried at $0 at
December 31, 1998 and March 31, 1999.


                                       5
<PAGE>   8


         Until September 1998, Applied was engaged in the separation of
hazardous waste through its 87% owned subsidiary, Commodore Separation
Technologies, Inc. ("Separation"). Effective September 28, 1998, Applied sold
its investments in Separation to Commodore Environmental Services, Inc.

         The preparation of consolidated financial statements in conformity with
generally accepted accounting principles requires management to make estimates
and assumptions that affect the reported amounts of assets and liabilities and
the disclosure of contingent assets and liabilities at the date of the financial
statements and the reported amounts of revenues and expenses during the
reporting period. Actual results could differ from those estimates.


Note B - Stockholders' Equity

         In 1997, Applied amended its Certificate of Incorporation authorizing
up to 10,000,000 shares of Preferred Stock, $.001 par value and increasing
authorized shares of Common Stock from 50,000,000 to 75,000,000.

Convertible Preferred Stock

         Effective September 28, 1998, Applied authorized and issued three new
series of Preferred Stock. Series B, C and D Preferred Stock were authorized up
to 25,000, 15,000, and 25,000 shares, respectively, all at $.001 par value. The
Company issued 20,909 of Series B, 10,189 of Series C and 20,391 of Series D
effective September 28, 1998.

         Each of the Series B, C and D Preferred Stock is convertible into
common shares of Applied; each has a par value of $.001 and a stated value of
$100 per share; each carries a dividend rate of $6.00 per share per annum from
the date of issuance, payable quarterly commencing December 31, 1998, when, and
if declared by the Board of Directors; and each has non-cumulative dividends.
Applied did not declare any dividend payment as of December 31, 1998 or March
31, 1999.

         The Series B, C and D Convertible Preferred Stock is convertible into
Common Stock at any time prior to redemption at a conversion rate of 142.9
shares of Common Stock for each share of Series B and D Convertible Preferred
Stock and 133.3 shares of Common Stock for each share of Series C Convertible
Preferred Stock (and effective conversion price of $.70 and $.75 per share of
Common Stock, respectively). The conversion price is subject to adjustment under
certain circumstances, including Applied taking action to change the number of
Common Shares outstanding, such as declaring a stock dividend.

         The holders of Convertible Preferred Stock have the right, voting as a
class, to approve or disapprove of the issuance of any class or series of stock
ranking senior to or on a parity with the Convertible Preferred Stock with
respect to declaration and payment of dividends or the distribution of assets on
liquidation, dissolution or winding-up. Upon liquidation, dissolution or
winding-up of Applied, holders of Convertible Preferred Stock are entitled to
receive liquidation distributions equivalent to $100.00 per share before any
distribution to holders of the Common Stock or any capital stock ranking junior
to the Convertible Preferred Stock.


Note C - Segment Information

         Using the guidelines set forth in SFAS No. 131, "Disclosures About
Segments of an Enterprise and Related Information," Applied has identified three
reportable segments in which it operates based on the services it provides. The
reportable segments are as follows: Commodore Advanced Sciences ("CASI"), which


                                       6
<PAGE>   9


primarily provides various engineering, legal, sampling and public relations
services to Government agencies on a cost plus basis; Solution , which is
developing and constructing equipment to treat mixed and hazardous waste through
a patented process using sodium and anhydrous ammonia; and through September 28,
1998, Separation, which provides water and contaminant separation by use of a
patented process. Common overhead costs are allocated between segments based on
a record of time spent by executives. Applied evaluates segment performance
based on the segment's net income (loss). Applied's foreign and export sales and
assets located outside of the United States are not significant. Summarized
financial information concerning Applied's reportable segments is shown in the
following table. Effective September 28, 1998, Applied sold its investment in
Separation to Commodore, and accordingly, the summarized information for
Separation is not included in the three months ended March 31, 1999.


THREE MONTHS ENDED MARCH 31, 1999

<TABLE>
<CAPTION>
                                                                            CORPORATE
                                                                             OVERHEAD
                                           TOTAL       CASI     SOLUTION    AND OTHER
<S>                                      <C>         <C>        <C>         <C>      
Contract Revenues                        $  3,345    $  3,345   $     --    $      --

Costs and expenses
     Cost of Sales                          3,004       3,004         --           --
     Research and Development                 285          --        285           --
     General and Administrative               751         247          5          499
     Depreciation and Amortization            187          26         90           71

                                         --------    --------   --------    ---------
              Total costs and expenses      4,227       3,277        380          570
                                         --------    --------   --------    ---------
Income (Loss) from Operations                (882)         68       (380)        (570)

     Interest Income                           17          --         --           17
     Interest Expense                         (15)         --         --          (15)
     Equity in losses of
         Unconsolidated subsidiary             --          --         --           --

                                         --------    --------   --------    ---------
Net Income (Loss)                        $   (880)   $     53   $   (380)   $    (553)
                                         ========    ========   ========    =========

Total Assets                             $ 14,056    $  3,145   $  2,094    $   8,817

Expenditures for long-lived assets       $    265    $     --   $    265    $      --
</TABLE>


                                       7
<PAGE>   10


THREE MONTHS ENDED MARCH 31, 1998

<TABLE>
<CAPTION>
                                                                                         CORPORATE
                                                                                         OVERHEAD
                                          TOTAL        CASI     SEPARATION   SOLUTION    AND OTHER
<S>                                      <C>         <C>         <C>         <C>         <C>     
Contract Revenues                        $  4,214    $  4,206    $     --    $     --    $      8

Costs and expenses
     Cost of Sales                          3,807       3,767          --          20          20
     Research and Development                 836          --         438         280         118
     General and Administrative             2,142         237         738          20       1,148
     Depreciation and Amortization            295          23          80         110          81
                                         --------    --------    --------    --------    --------
              Total costs and expenses      7,080       4,027       1,256         430       1,367
                                         --------    --------    --------    --------    --------
Income (Loss) from Operations              (2,866)        179      (1,256)       (430)     (1,359)

     Interest Income                          163          --          53          --         110
     Interest Expense                        (244)        (27)         --          --        (217)
     Equity in losses of
         Unconsolidated subsidiary           (448)         --          --          --        (448)
                                         --------    --------    --------    --------    --------
Net Income (Loss)                        $ (3,395)   $    152    $ (1,203)   $   (430)   $ (1,914)
                                         ========    ========    ========    ========    ========

Total Assets                             $ 30,093    $  4,371    $  5,166    $  1,126    $ 19,430

Expenditures for long-lived assets       $    362    $      2    $    106    $    254    $     --
</TABLE>


Note D - Contingencies

         Applied has matters of litigation arising in the ordinary course of
business which in the opinion of management will not have a material adverse
effect on its financial condition or results of operations.


Note E - Acquisition

         In March 1999, Applied entered into a Letter of intent with Global
Energy Investors, LLC ("Global"). Under the terms of the Letter of Intent,
Applied will acquire a 50% interest in Global for $5.0 million worth of Applied
Convertible Preferred Stock and $2.5 million in cash. The Convertible Preferred
Stock will have a conversion price of $.50 per share, will be non-dividend
bearing and Global will be obligated to convert the Preferred Stock into
Applied's Common Stock upon the earlier of March 31, 2001 or when Applied's
Common Stock trades above $.50 per share for twenty days. Applied will also be
obligated to acquire the remaining 50% interest of Global from the Global
shareholders for 12.5 million shares of Applied's Common Stock at such time that
Applied's Common Stock trades for at least $2.00 per share for twenty days. In
April, 1999, both parties signed a definitive agreement with substantially the
same terms as outlined in the Letter of Intent. Applied's acquisition of Global
is conditional upon due diligence and the raising of $10 million in new working
capital for Applied and Global.



                                       8
<PAGE>   11


ITEM 2.  MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION

         AND RESULTS OF OPERATION 

Overview

         Commodore Applied Technologies, Inc. and subsidiaries ("Applied"), is
engaged in the destruction and neutralization of hazardous waste from other
materials. Applied owns technologies related to the separation and destruction
of polychlorinated biphenyls (PCBs) and chlorofluorocarbons (CFCs).

         Applied is currently working on the commercialization of these
technologies through development efforts, licensing arrangements and joint
ventures. Through Commodore Advanced Sciences, Inc. ("CASI"), formerly Advanced
Sciences, Inc., a subsidiary acquired on October 1, 1996, Applied has contracts
with various government agencies and private companies in the United States and
abroad. As some government contracts are funded in one-year increments, there is
a possibility for cutbacks as these contracts constitute a major portion of
CASI's revenues, and such a reduction would materially affect the operations.
However, management believes the subsidiary's existing client relationships will
allow Applied to obtain new contracts in the future.


RESULTS OF OPERATIONS

Three Months Ended March 31, 1999 Compared to Three Months Ended March 31, 1998

         Revenues were $3,345,000 for the three months ended March 31, 1999,
compared to $4,214,000 for the three months ended March 31, 1998. Such revenues
were primarily from the Company's ASI subsidiary, and consisted of engineering
and scientific services performed for the United States government under a
variety of contracts, most of which provide for reimbursement of cost plus fixed
fees. Revenue under cost-reimbursement contracts is recorded under the
percentage of completion method as costs incurred and include estimated fees in
the proportion that costs to date bear to total estimated costs. The Company has
seen some reduction in annual sales volume since the middle of 1998 when ASI's
major customer was forced to separately bid some professional services that were
originally subcontracted through ASI. This occurred because the dollar volume of
work had grown past the level where it could be subcontracted. Cost of sales
decreased from $3,807,000 to $3,004,000 for the same period. This decrease is
consistent with the decrease in revenue.

         For the three months ended March 31, 1999, the Company incurred
research and development costs of $285,000 as compared to $836,000 for the three
months ended March 31, 1998. In 1998, some personnel previously charged to
research and development were reassigned to the Company project in Weldon
Spring. Research and development costs include salaries, wages, and other
related costs of personnel engaged in research and development activities,
contract services and materials, test equipment and rent for facilities involved
in research and development activities. Research and development costs are
expensed when incurred, except that those costs related to the design or
construction of an asset having an economic useful life are capitalized, and
then depreciated over the estimated useful life of the asset. Commodore
Separation Technologies, Inc. ("Separation"), a former subsidiary, had research
and development costs of $438,000 for the three months ended March 31, 1998.

         General and administrative expenses for the three months ended March
31, 1999 were $751,000 as compared to $2,142,000 for the three months ended
March 31, 1998. Separation had General and Administration costs of $738,000 for
the three months ended March 31, 1998. The savings in 1999 are a result of
restructuring steps taken during the last half of 1998.


                                       9
<PAGE>   12


         Interest income was $17,000 for the three months ended March 31, 1999,
as compared to $163,000 for the three months ended March 31, 1998. This decrease
is consistent with the reduction in cash balances available for investment as
funds were used to pay ongoing expenses.

         Interest expense for the three months ended March 31, 1999 was $15,000
as compared to $244,000 for the three months ended March 31, 1998. Interest
changes in 1999 result from favorable rate and terms on a line of credit put in
place in April, 1998.

         Equity in losses of unconsolidated subsidiary for the three months
ended March 31, 1999 was $0 as compared to $448,000 for the three months ended
March 31, 1998. The Company's Teledyne-Commodore, LLC joint venture commenced
operations in October 1996. The Company recorded its liability for all capital
contributions at December 31, 1998. The Company currently has no plans to
contribute any further capital to the LLC.


LIQUIDITY AND CAPITAL RESOURCES

         From its inception through the second quarter of 1996, the Company's
operations were financed principally by loans and investments from its
stockholders. In June 1996, the Company successfully completed its IPO from
which it received net proceeds of approximately $30,500,000. The Company
allocated approximately $12.0 million of the net proceeds for the funding of
proposed collaborative joint ventures, $2.0 million of which was allocated to
Teledyne-Commodore, LLC.

         In July 1996, the Company utilized a portion of the net proceeds from
its IPO to repay an outstanding line of credit of $2.0 million, as well as a
$5,925,426 promissory note to its principal stockholder, Commodore Environmental
Services, Inc. ("Environmental") . The Company set aside $1.0 million cash
collateral to support a loan made by a commercial bank to the Company's
principal stockholder in December 1993. In September 1996, such cash collateral
was released by the bank.

         In August 1996, the Company loaned $1.5 million to Lanxide Performance
Materials, Inc. ("LPM"), a wholly-owned subsidiary of Lanxide Corporation, a
Delaware Corporation ("Lanxide"). Lanxide is related to the Company by
significant common beneficial ownership. The LPM Note is collateralized by the
assets of LPM and guaranteed by Lanxide. The LPM Note became due on February 28,
1998. In March 1998, the Company transferred the LPM Note to Environmental,
together with $500,000 in cash, as partial prepayment of the $4.0 million
unsecured loan from Environmental to the Company in September 1997.

         In December 1996, the Company acquired (i) all of the outstanding
capital stock of Separation and (ii) all of the outstanding capital stock of CFC
Technologies from Environmental, as part of a corporate restructuring of
Environmental to consolidate all of its current environmental technology
businesses with the Company. In addition, Environmental assigned to the Company
outstanding Separation notes aggregating $976,200 at December 2, 1996,
representing advances previously made by Environmental to Separation, which the
Company has contributed to the equity of Separation. In consideration for the
transfer of all of the outstanding capital stock of Separation and CFC
Technologies to the Company, the Company paid Environmental $3.0 million in cash
and issued to Environmental a warrant expiring December 2, 2003 to purchase
7,500,000 shares of Company Common Stock at an exercise price of $15.00 per
share, valued at $2.4 million.

         In April 1997, Separation completed an initial public offering of its
equity securities, from which it received net proceeds of approximately
$11,100,000. Such funds were used primarily to finance Separation's operations
through 1998.


                                       10
<PAGE>   13


         In August 1997, the Company completed the August 1997 Private Placement
from which it received net proceeds of approximately $1.6 million. In connection
with the sale, the Company incurred cash transaction costs of approximately
$117,000 and issued warrants, expiring on August 15, 2002, to the placement
agent.

         In October 1997, the Company completed the October 1997 Private
Placement from which it received aggregate net proceeds of approximately $2.4
million. In connection with the October 1997 Private Placement, the Company
incurred cash transaction costs of approximately $209,000 and issued warrants,
expiring on September 30, 2002, to the placement agent.

         In September 1997, Environmental provided the Company with a $4.0
million unsecured loan, evidenced by the Convertible Note due August 31, 2002.
In connection with the Convertible Note, the Company issued warrants to purchase
1,000,000 shares of Common Stock to Environmental valued at $660,000 and
provided a beneficial conversion privilege with an intrinsic value of $750,000
as of the date of the transaction. In March 1998, the Company prepaid $2.0
million of the Convertible Note by (i) paying Environmental the sum of $500,000
in cash and (ii) transferring to Environmental the LPM promissory note, dated
August 30, 1996, in the principal amount of $1.5 million. Lanxide, which
specializes in the manufacture of ceramic bonding and refractory materials, is
related to the Company by significant common beneficial ownership. To induce
Environmental to accept the Company's prepayment of $2.0 million of the
Convertible Note (and thereby give up the right to convert $2.0 million of the
Convertible Note into Common Stock), the Company issued to Environmental an
additional warrant to purchase up to 514,000 shares of Common Stock at an
exercise price of $4.50 per share. Such exercise price was fixed at
approximately 110% of the closing sale price of the Common Stock on February 20,
1998, the trading day immediately prior to the date the Board of Directors of
the Company approved such prepayment. The estimated fair value of such warrant
is approximately $340,000. The remaining balance of this Intercompany
Convertible Note was paid off by December 31, 1998.

         At March 31, 1999 and December 31,1998, CASI had a $388,000 and
$361,000 outstanding balance, respectively, on its revolving lines of credit. In
August 1998, CASI refinanced their line of credit. The line of credit is not to
exceed 75% of eligible receivable or $2,000,000 and is due August 4, 2000 with
interest payable monthly at prime plus 1.5 percent (9.25 percent as of March 31,
1999). The credit line is collateralized by the assets of CASI and is guaranteed
by Applied. This line of credit contains certain financial covenants and
restrictions including minimum ratios that CASI must satisfy. CASI was in
compliance with the covenants at March 31, 1999 and December 31, 1998.

         In addition, the line of credit agreement stipulates that no payments
shall be made to the Company other than monthly scheduled payments of principal
with respect to $6,300,000 of subordinated indebtedness owed by ASI to the
company (which is eliminated in consolidation) and intercompany indebtedness not
to exceed $20,000 in any month. In addition, CASI shall not incur indebtedness
in excess of $25,000, other than trade payables, the above subordinated
indebtedness and other contractual obligations to suppliers and customers
incurred in the ordinary course of business.

         In February 1998, Environmental provided the Company with a $5,450,000
uncollateralized loan, evidenced by the Intercompany Note due on the earlier to
occur of (a) December 31, 1999, or (b) consummation of any public offering or
private placement of securities of the Company with net proceeds aggregating in
excess of $6.0 million, other than in respect of working capital financing or
secured financing of assets received by the Company in the ordinary course of
business from any bank or other lending institution, subject to certain
conditions. The Company has used the net proceeds of the loan solely for working
capital and general corporate purposes and not for the satisfaction of any
portion of Company debt or to redeem any Company equity or equity-equivalent
securities. During 1998, the Company repaid $828,000 of the principle balance on
this Note before the Note was paid off in its entirety through the September 28,
1998 transaction described below. In connection with the loan, the Company
amended and restated in its entirety a five-year warrant to purchase


                                       11
<PAGE>   14


7,500,000 shares of Common Stock issued to Environmental on December 2, 1996 to,
among other things, reduce the exercise price of the warrant from $15.00 per
share to $10.00 per share. In addition, the Company issued to Environmental an
additional five-year warrant to purchase 1,500,000 shares of Common Stock at an
exercise price of $10.00 per share.

         Effective September 28, 1998, the Company repaid $6,756,000 of its debt
to Environmental (representing the balances on the September, 1997 Convertible
Note and the February, 1998 Intercompany Note) by exchanging the debt for (i)
10,000,000 shares of Separation Common Stock (as repayment of $1,250,000 of
debt; (ii) 20,909 shares of newly created 6% Series B Convertible Preferred
Stock of the Company (as repayment of $2,090,870 of debt); (iii) 10,189 shares
of newly created 6% Series C Convertible Preferred Stock of the Company (as
repayment of $1,018,864 of debt); (iv) 20,391 shares of newly created 6% Series
D Convertible Preferred Stock of the Company (as repayment of $2,039,100 of
debt); (v) assignment to Environmental of an account receivable due to the
Company from Separation in the amount of $357,000 (as repayment of $357,000 of
debt); and (vi) amendment of an existing warrant owned by Environmental to
purchase 1,500,000 shares of the Company's Common Stock at $10.00 per share,
reducing the exercise price to $1.50 per share. The terms of the debt
restructuring were determined as a result of arm's length negotiations between
representatives of both the Company and Environmental, and were supported by
fairness opinions by an independent, third-party appraiser. Environmental
currently owns approximately 35% of the outstanding shares of the Company's
common stock.

         As part of this restructuring plan, the Company consummated the
transfer of all 10,000,000 of its shares of Common Stock, par value $.001 per
share (the "Separation Stock"), of Separation, representing approximately 87% of
the issued and outstanding shares of capital stock of Separation to Commodore
Environmental Services LLC, a Delaware limited liability company wholly owned by
Commodore. The transfer is effective as of September 28, 1998. Accordingly, the
1998 consolidated financial statements of the Company, include the activity of
Separation only through September 28, 1998. As a result of this sale, the
Company recognized a gain of $4,664,000. The 1999 Condensed Consolidated
Financial Statements reflect no activity for Separation.

         Also, the Company has entered into a definitive agreement to purchase
Global Energy Investors, LLC ("GEI"). The Company believes that this transaction
will be received positively by the investment community and will allow the
merged companies to raise $10,000,000 in new equity capital. This transaction is
scheduled to be completed in the third quarter of 1999.

         For the three months ended March 31, 1999, the Company incurred a net
loss of $880,000 as compared to a net loss of $3,395,000 for the three months
ended March 31, 1998. For the years ended December 31, 1998, 1997 and 1996, the
Company incurred losses exclusive of their gain on the sale of affiliate and
extraordinary item of $13,353,000, $15,694,000 and $5,643,000,respectively. The
Company has also experienced net cash outflows from operating activities of
$9,155,000, $8,220,000 and $7,159,000 for the years ended December 31, 1998,
1997 and 1996, respectively. At December 31, 1998, 1997 and 1996 the Company had
working capital of $1,817,000, $11,170,000 and $8,838,000, respectively, and
stockholders' equity of $11,908,000, $11,654,000 and $20,076,000, respectively.
The Company's decrease in working capital and stockholders' equity from December
31, 1996 to December 31, 1998 is principally due to the net loss for the period.

         Although the Company believes its capital requirements for the
remainder of 1999 will be met through the development of its business, the
Company will be required to obtain financing through external sources. The
Company is currently looking at various alternatives to fund its cash needs
until its operations generate an adequate positive cash flow. It is the intent
of the Company to have its subsidiary, Advanced Sciences, begin repayment of an
intercompany loan by borrowing funds through its line of credit to maximize use
of the funds available under the line of credit. The Company anticipates that
the funds available from full utilization of the line of credit are
approximately $500,000. Also, the Company is in final negotiations to complete
an equipment financing loan which will provide the Company with approximately


                                       12
<PAGE>   15

$1,400,000 working capital and sufficient funds to complete a second S10 (SET
technology, 10 ton a day) unit. This financing should be available in the second
quarter of 1999. There can be no assurance that such financing will be available
or, if available, that it will be on terms satisfactory to the Company.


NET OPERATING LOSS CARRYFORWARDS

         The Company has net operating loss carryforwards of approximately
$31,000,000, which expire in the years 2000 through 2018. The amount of net
operating loss carryforward that can be used in any one year will be limited by
the applicable tax laws which are in effect at the time such carryforward can be
utilized. A full valuation allowance has been established to offset any benefit
from the net operating loss carryforwards. It cannot be determined when or if
the Company will be able to utilize the net operating losses.


YEAR 2000 CONSIDERATIONS

         Many existing computer systems and software products are coded to
accept only two-digit entries in the date code field. As the year 2000
approaches, these code fields will need to accept four digit entries to
distinguish between years beginning with "19" from those beginning with "20." As
a result, in less than two years, computer systems and/or software products used
by many companies may need to be upgraded to comply with such year 2000
requirements. If uncorrected, many computer applications could fail or create
erroneous results by or at the year 2000.

         The Company believes that its mainframe database and operating systems
are year 2000 compliant, meaning that they may be able to operate without error
in dates and date-related data, including calculating, comparing, indexing and
sequencing, prior to on and after January 1, 2000. However, certain of the
Company's software applications utilized to bill customers and maintain finance
and accounting records are coded using two digits rather than four to define the
applicable year. The Company is working with its major software vendor to assure
that proper modifications will be made to such applications and anticipates such
modifications will be completed by June 1999. The Company also relies, directly
and indirectly, on external systems of its customers (primarily U.S. government
agencies and contractors), suppliers, creditors, financial organizations and
governmental entities. Consequently, the Company could be affected through the
disruptions in the operations of the enterprises with which the Company
interacts. Furthermore, the purchasing frequency and volume of customers or
potential customers may be affected by year 2000 issues as companies expend
significant resources to make their current systems year 2000 compliant.

         The Company has not quantified the total costs required to become year
2000 compliant, but does not expect that the cost of addressing any year 2000
issues will be a material event or uncertainty that would cause its reported
financial information not to be necessarily indicative of future operating
results or future financial condition, or that the costs or consequences of
incomplete or untimely resolution of any year 2000 issue represent a known
material event or uncertainty that is reasonably likely to affect its future
financial results, or cause its reported financial information not to be
necessarily indicative of future operating results or future financial
condition. As of March 31, 1999, the total costs incurred to address the
Company's year 2000 issues have not been material (approximately $61,500).
However, if the Company, its customers or vendors encounter any unanticipated
delays in, or costs associated with, the resolution of any year 2000 issue, the
Company's business, financial condition and results of operations could be
materially adversely affected. Accordingly, the Company plans to devote the
necessary resources to becoming year 2000 compliant in a timely manner and
intends to create a contingency plan by July 1999 to handle any year 2000
problems.


                                       13
<PAGE>   16


FORWARD-LOOKING STATEMENTS

         Certain matters discussed in this Quarterly Report are "forward-looking
statements" intended to qualify for the safe harbors from liability established
by Section 27A of the Securities Act and Section 21E of the Securities Exchange
Act of 1934, as amended (the "Exchange Act"). These forward-looking statements
can generally be identified as such because the context of the statement will
include words such as the Company "believes," "anticipates," "expects" or words
of similar import. Similarly, statements that describe the Company's future
plans, objectives or goals are also forward-looking statements. Such statements
may address future events and conditions concerning, among other things, the
Company's results of operations and financial condition; the consummation of
acquisition and financing transactions and the effect thereof on the Company's
business; capital expenditures; litigation; regulatory matters; and the
Company's plans and objectives for future operations and expansion. Any such
forward-looking statements would be subject to the risks and uncertainties that
could cause actual results of operations, financial condition, acquisitions,
financing transactions, operations, expenditures, expansion and other events to
differ materially from those expressed or implied in such forward-looking
statements. Any such forward-looking statements would be subject to a number of
assumptions regarding, among other things, future economic, competitive and
market conditions generally. Such assumptions would be based on facts and
conditions as they exist at the time such statements are made as well as
predictions as to future facts and conditions, the accurate prediction of which
may be difficult and involve the assessment of events beyond the Company's
control. Further, the Company's business is subject to a number of risks that
would affect any such forward-looking statements. These risks and uncertainties
include, but are not limited to, the ability of the Company to commercialize its
technology; product demand and industry pricing; the ability of the Company to
obtain patent protection for its technology; developments in environmental
legislation and regulation; the ability of the company to obtain future
financing on favorable terms; and other circumstances affecting anticipated
revenues and costs. These risks and uncertainties could cause actual results of
the Company to differ materially from those projected or implied by such
forward-looking statements.


                                       14
<PAGE>   17


                           PART II - OTHER INFORMATION

ITEM 1.  LEGAL PROCEEDINGS

                  There have been no material legal proceedings to which the
Company is a party which have not been disclosed in previous filings with the
Securities and Exchange Commission. There are no material developments to be
reported in any previously reported legal proceedings.

ITEM 2.  CHANGE IN SECURITIES

         Not applicable.

ITEM 3.  DEFAULTS AMONG SENIOR SECURITIES

         Not applicable.

ITEM 4.  SUBMISSION OF  MATTERS TO A VOTE OF SECURITY HOLDERS

         Not applicable.

ITEM 5.  OTHER EVENTS

         Not applicable.

ITEM 6.  EXHIBITS AND REPORTS ON FORM 8-K

         (a)      Exhibits - none

         (b)      Reports on Form 8-K - none


                                       15
<PAGE>   18


                                   SIGNATURES


Pursuant to the requirements of the Securities Exchange Act of 1934, the
registrant has duly caused this report to be signed on its behalf by the
undersigned thereunto duly authorized.







DATE: MAY 14, 1999                  COMMODORE APPLIED TECHNOLOGIES, INC.
                                    (REGISTRANT)


                                    BY     /s/ JAMES M. DE ANGELIS
                                      ------------------------------------------
                                       JAMES M. DE ANGELIS -  VICE PRESIDENT AND
                                       TREASURER (AS BOTH A DULY AUTHORIZED
                                       OFFICER OF THE REGISTRANT AND THE 
                                       PRINCIPAL FINANCIAL OFFICER OF THE
                                       REGISTRANT)


                                       16

<PAGE>   19

                               INDEX TO EXHIBITS


<TABLE>
<CAPTION>
EXHIBIT
NUMBER              DESCRIPTION
-------             -----------
<S>               <C>
  27              Financial Data Schedule.
</TABLE>