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SECURITIES AND EXCHANGE COMMISSION
 Washington, D.C. 20549
 FORM 10-Q/A
 (Amendment No. 1)
 (Mark One)
 þ
    
    QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 For the quarterly period (13 weeks) ended October 29, 2005
 OR
 o
    
    TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 For the transition period from ___to ___
 Commission file number 1-10876
 SHOPKO STORES, INC.
  Wisconsin
    
    41-0985054(State or other jurisdiction
of
incorporation or organization)
    
    (I.R.S. Employer Identification No.)
 700 Pilgrim Way, Green Bay, Wisconsin
    
    54304(Address of principal executive offices)
    
    (Zip Code)
 (920)429-2211
   
  þ o
  þ o
  o þ
  Title of Each Class
    
    Shares OutstandingCommon Shares
    
    30,266,726Exhibit Index on Page 16
    
    Page 1 of Page 23




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PagePart IItem 1  Financial StatementsCondensed Consolidated Statements of Operations for the 13 weeks ended October 29, 2005 and October 30, 2004
    
    
    4Condensed Consolidated Statements of Operations for the 39 weeks ended October 29, 2005 and October 30, 2004
    
    
    5Condensed Consolidated Balance Sheets as of October 29, 2005, October 30, 2004 and January 29, 2005
    
    
    6Condensed Consolidated Statements of Cash Flows for the 39 weeks ended October 29, 2005 and October 30, 2004
    
    
    7Condensed Consolidated Statement of Shareholders Equity for the 39 weeks ended October 29, 2005
    
    
    8Notes to Condensed Consolidated Financial Statements
    
    
    9-13Part IIItem 6  Exhibits
    
    
    14Signatures
    
    
    15Certification of Sr. VP, CFO and Co-CEOCertification of President and Co-CEOCertification of Sr. VP, Chief Merchandising Officer and Co-CEOStatement of Sr VP, CFO and Co-CEOCertification of President and Co-Chief Executive OfficerStatement of Sr. VP, Chief Merchandising Officer and Co-CEO
 2




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EXPLANATORY NOTES
    3




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PART I  FINANCIAL INFORMATION
 
 Item 1: Financial Statements
 
 CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
 ShopKo Stores, Inc. and Subsidiaries
    
    Third Quarter (13 Weeks) Ended(In thousands, except per share data)October 29,
    
    
    October 30,2005
    
    
    2004(UNAUDITED)
    
    
    (UNAUDITED)Revenues:Net sales
    
    $
    704,845
    
    
    $
    746,391Licensed department rentals and other income
    
    
    3,425
    
    
    
    3,497708,270
    
    
    
    749,888Costs and expenses:Cost of sales
    
    
    511,843
    
    
    
    554,175Selling, general and administrative expenses
    
    
    168,136
    
    
    
    162,684Depreciation and amortization expenses
    
    
    19,739
    
    
    
    20,916Merger-related expenses
    
    
    16,256
    
    
    
    715,974
    
    
    
    737,775(Loss) income from operations
    
    
    (7,704
    )
    
    
    12,113Interest expense
    
    
    6,785
    
    
    
    8,840(Loss) income before income taxes
    
    
    (14,489
    )
    
    
    3,273Income tax (benefit) provision
    
    
    (383
    )
    
    
    1,278Net (loss) income
    
    $
    (14,106
    )
    
    $
    1,995Net (loss) income per share of common stock:Basic
    
    $
    (0.47
    )
    
    $
    0.07Diluted
    
    $
    (0.47
    )
    
    $
    0.07Weighted average number of common shares outstanding:Basic
    
    
    30,211
    
    
    
    29,362Diluted
    
    
    30,211
    
    
    
    29,683
  4




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CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
 ShopKo Stores, Inc. and Subsidiaries
    
    Year to Date (39 Weeks) Ended(In thousands, except per share data)October 29,
    
    
    October 30,2005
    
    
    2004(UNAUDITED)
    
    
    (UNAUDITED)Revenues:Net sales
    
    $
    2,145,099
    
    
    $
    2,257,000Licensed department rentals and other income
    
    
    10,384
    
    
    
    9,8472,155,483
    
    
    
    2,266,847Costs and expenses:Cost of sales
    
    
    1,558,989
    
    
    
    1,677,679Selling, general and administrative expenses
    
    
    489,695
    
    
    
    486,630Depreciation and amortization expenses
    
    
    61,265
    
    
    
    63,574Merger-related expenses
    
    
    19,095
    
    
    
    2,129,044
    
    
    
    2,227,883Income from operations
    
    
    26,439
    
    
    
    38,964Interest expense
    
    
    21,148
    
    
    
    25,985Income before income taxes
    
    
    5,291
    
    
    
    12,979Income tax provision
    
    
    7,235
    
    
    
    5,064Net (loss) income
    
    $
    (1,944
    )
    
    $
    7,915Net (loss) income per share of common stock:Basic
    
    $
    (0.06
    )
    
    $
    0.27Diluted
    
    $
    (0.06
    )
    
    $
    0.27Weighted average number of common shares outstanding:Basic
    
    
    30,004
    
    
    
    29,288Diluted
    
    
    30,004
    
    
    
    29,553
  5




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CONDENSED CONSOLIDATED BALANCE SHEETS
 ShopKo Stores, Inc. and Subsidiaries
    
    Third quarter as of
    
    
    Fiscal Year End(In thousands)October 29,
    
    
    October 30,
    
    
    January 29,2005
    
    
    2004
    
    
    2005 *(UNAUDITED)
    
    
    (UNAUDITED)ASSETSCurrent assets:Cash and cash equivalents
    
    $
    33,215
    
    
    $
    29,280
    
    
    $
    25,110Receivables,
less allowance for losses of $2,149,
$2,438 and $1,833, respectively
    
    
    50,574
    
    
    
    55,398
    
    
    
    62,019Merchandise inventories
    
    
    646,832
    
    
    
    701,953
    
    
    
    564,099Other current assets
    
    
    6,646
    
    
    
    8,241
    
    
    
    9,046Total current assets
    
    
    737,267
    
    
    
    794,872
    
    
    
    660,274Other assets and deferred charges
    
    
    8,904
    
    
    
    7,943
    
    
    
    9,037Intangible assets, net of accumulated amortization of
$15,873, $12,825 and $13,330, respectively
    
    
    22,877
    
    
    
    28,984
    
    
    
    21,865Property and equipment, net of accumulated
depreciation of $868,403, $828,447 and
$828,768; impairment reserve of $686, $4,004
and $1,660, respectively
    
    
    687,541
    
    
    
    757,254
    
    
    
    742,027Total assets
    
    $
    1,456,589
    
    
    $
    1,589,053
    
    
    $
    1,433,203LIABILITIES AND SHAREHOLDERS EQUITYCurrent liabilities:Short-term debt
    
    $
    65,000
    
    
    $
    156,101
    
    
    $
    85,679Accounts payable  trade
    
    
    280,323
    
    
    
    297,489
    
    
    
    225,777Accrued compensation and related taxes
    
    
    34,427
    
    
    
    37,287
    
    
    
    37,088Deferred taxes and other accrued liabilities
    
    
    112,534
    
    
    
    113,873
    
    
    
    104,903Accrued income and other taxes
    
    
    33,209
    
    
    
    29,087
    
    
    
    49,760Current portion of long-term obligations and leases
    
    
    6,288
    
    
    
    62,304
    
    
    
    8,018Total current liabilities
    
    
    531,781
    
    
    
    696,141
    
    
    
    511,225Long-term obligations and leases, less current portion
    
    
    230,297
    
    
    
    240,637
    
    
    
    238,612Other long-term obligations
    
    
    23,975
    
    
    
    21,838
    
    
    
    21,976Deferred income taxes
    
    
    22,039
    
    
    
    29,791
    
    
    
    22,963Shareholders equity:Common stock
    
    
    322
    
    
    
    314
    
    
    
    316Additional paid-in capital
    
    
    408,296
    
    
    
    394,016
    
    
    
    396,514Retained earnings
    
    
    280,587
    
    
    
    246,882
    
    
    
    282,261Less treasury stock
    
    
    (40,708
    )
    
    
    (40,566
    )
    
    
    (40,664
    )Total shareholders equity
    
    
    648,497
    
    
    
    600,646
    
    
    
    638,427Total liabilities and shareholders equity
    
    $
    1,456,589
    
    
    $
    1,589,053
    
    
    $
    1,433,203
 
 *
    
    Condensed from audited financial statements.  6




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CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
 ShopKo Stores, Inc. and Subsidiaries
    
    Year to Date (39 weeks) Ended(In thousands)October 29,
    
    
    October 30,2005
    
    
    2004(UNAUDITED)
    
    
    (UNAUDITED)Cash flows from operating activities:Net (loss) income
    
    $
    (1,944
    )
    
    $
    7,915Adjustments to reconcile net income to net
cash provided by operating activities:Depreciation and amortization
    
    
    61,265
    
    
    
    63,574Impairment charges
    
    
    570
    
    
    
    672Gain on sale of property and equipment
    
    
    (4,106
    )
    
    
    (2,821
    )Deferred income taxes
    
    
    3,380
    
    
    
    6,987Change in assets and liabilities:Receivables
    
    
    11,445
    
    
    
    7,410Merchandise inventories
    
    
    (82,733
    )
    
    
    (132,637
    )Other current assets
    
    
    2,400
    
    
    
    2,634Other assets
    
    
    2,118
    
    
    
    831Accounts payable
    
    
    54,546
    
    
    
    44,176Accrued liabilities
    
    
    (13,944
    )
    
    
    (12,702
    )Other long-term obligations
    
    
    1,999
    
    
    
    (3,367
    )Net cash provided by (used in) operating activities
    
    
    34,996
    
    
    
    (17,328
    )Cash flows from investing activities:Purchases of property and equipment
    
    
    (20,490
    )
    
    
    (50,799
    )Proceeds from the sale of property and equipment
    
    
    18,768
    
    
    
    14,948Net payments for pharmacy customer lists
    
    
    (3,281
    )
    
    
    (7,410
    )Net cash (used in) investing activities
    
    
    (5,003
    )
    
    
    (43,261
    )Cash flows from financing activities:Proceeds from short-term borrowings
    
    
    0
    
    
    
    73,832Payments of debt and capital lease obligations
    
    
    (31,596
    )
    
    
    (8,119
    )Sale of common stock due to exercise of stock options
    
    
    9,752
    
    
    
    1,622Purchase of treasury stock
    
    
    (44
    )
    
    
    (252
    )Net cash (used in) provided by financing activities
    
    
    (21,888
    )
    
    
    67,083Net increase in cash and cash equivalents
    
    
    8,105
    
    
    
    6,494Cash and cash equivalents at beginning of period
    
    
    25,110
    
    
    
    22,786Cash and cash equivalents at end of period
    
    $
    33,215
    
    
    $
    29,280
  7




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CONDENSED CONSOLIDATED STATEMENT OF SHAREHOLDERS EQUITY
 ShopKo Stores, Inc. and Subsidiaries(In thousands)
    
    (UNAUDITED)AdditionalCommon Stock
    
    Paid-in
    
    Retained
    
    Treasury Stock
    
    TotalShares
    
    Amount
    
    Capital
    
    Earnings
    
    Shares
    
    Amount
    
    Shares
    
    AmountBALANCES AT JANUARY 29, 2005
    
    
    31,580
    
    
    $
    316
    
    
    $
    396,514
    
    
    $
    282,261
    
    
    
    (1,930
    )
    
    $
    (40,664
    )
    
    
    29,650
    
    
    $
    638,427Net (loss)
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (1,944
    )
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (1,944
    )Issuance of restricted stock
    
    
    10
    
    
    
    
    
    
    
    219
    
    
    
    (219
    )
    
    
    
    
    
    
    
    
    
    
    10
    
    
    
    -0-Forfeiture of restricted stock
    
    
    (25
    )
    
    
    
    
    
    
    (325
    )
    
    
    325
    
    
    
    
    
    
    
    
    
    
    
    (25
    )
    
    
    -0-Sales of common stock under
option plans
    
    
    630
    
    
    
    6
    
    
    
    9,746
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    630
    
    
    
    9,752Income tax benefit related to
stock options
    
    
    
    
    
    
    
    
    
    
    2,142
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    2,142Restricted stock expense
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    164
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    164Purchase of treasury stock
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (2
    )
    
    
    (44
    )
    
    
    (2
    )
    
    
    (44
    )BALANCES AT OCTOBER 29, 2005
    
    
    32,195
    
    
    $
    322
    
    
    $
    408,296
    
    
    $
    280,587
    
    
    
    (1,932
    )
    
    $
    (40,708
    )
    
    
    30,263
    
    
    $
    648,497
  8




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NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS  Unaudited)
 A. Interim Financial Statements
    B. Restructuring Reserve
    9




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Lease termination andproperty carrying costsBalance as of January 29, 2005
    
    $
    13,329Cash Payments
    
    
    884Balance as of October 29, 2005
    
    $
    12,445
 C. Stock-Based Employee Compensation Plans
   Third Quarter
    
    
    Year to Date(13 Weeks) Ended
    
    
    (39 Weeks) EndedOct 29,
    
    
    Oct 30,
    
    
    Oct 29,
    
    
    Oct 30,2005
    
    
    2004
    
    
    2005
    
    
    2004Net (loss) income as reported
    
    $
    (14,106
    )
    
    $
    1,995
    
    
    $
    (1,944
    )
    
    $
    7,915Add: Stock-based employee
compensation expense
included in reported net
income, net of related tax effects
    
    
    44
    
    
    
    114
    
    
    
    101
    
    
    
    309Deduct: Total stock-based
employee compensation
expense determined under
fair value method for all
share and option awards, net
of related tax effects
    
    
    (394
    )
    
    
    (625
    )
    
    
    (1,008
    )
    
    
    (1,773
    )Pro forma net (loss) income
    
    $
    (14,456
    )
    
    $
    1,484
    
    
    $
    (2,851
    )
    
    $
    6,451Net (loss) income per share:Basic  as reported
    
    $
    (0.47
    )
    
    $
    0.07
    
    
    $
    (0.06
    )
    
    $
    0.27Basic  pro forma
    
    $
    (0.48
    )
    
    $
    0.05
    
    
    $
    (0.10
    )
    
    $
    0.22Diluted  as reported
    
    $
    (0.47
    )
    
    $
    0.07
    
    
    $
    (0.06
    )
    
    $
    0.27Diluted  pro forma
    
    $
    (0.48
    )
    
    $
    0.05
    
    
    $
    (0.10
    )
    
    $
    0.22
 10




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D. Business Segment Information
    Third Quarter (13 Weeks) Ended
    
    
    Year to Date (39 Weeks) EndedOctober 29,
    
    
    October 30,
    
    
    October 29,
    
    
    October 30,2005
    
    
    2004
    
    
    2005
    
    
    2004Net salesShopKo Retail
    
    $
    522,152
    
    
    $
    553,134
    
    
    $
    1,573,260
    
    
    $
    1,674,734Pamida Retail
    
    
    182,693
    
    
    
    193,257
    
    
    
    571,839
    
    
    
    582,266Total net sales
    
    $
    704,845
    
    
    $
    746,391
    
    
    $
    2,145,099
    
    
    $
    2,257,000Earnings (loss) from
operationsShopKo Retail
    
    $
    13,781
    
    
    $
    18,466
    
    
    $
    55,036
    
    
    $
    55,625Pamida Retail
    
    
    2,024
    
    
    
    (351
    )
    
    
    11,538
    
    
    
    3,378Corporate
    
    
    (23,509
    )
    
    
    (6,002
    )
    
    
    (40,135
    )
    
    
    (20,039
    )Earnings (loss) from
operations
    
    $
    (7,704
    )
    
    $
    12,113
    
    
    $
    26,439
    
    
    $
    38,964
  E. Commitments & Contingencies
  F. Merger
  11




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plus
  G. Long-Term Debt
   Federated Bond Fund, a portfolio of Federated
Investment Series Funds, Inc., et. al. v. ShopKo Stores, Inc., et. al.
 12




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pari passu
 H. Litigation
 In re
ShopKo Shareholder Litigation
  13




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PART II  OTHER INFORMATION
 
 Item 6 : Exhibits
        
 *
    
    The office of Chief Executive Officer is comprised of three executive officers, each serving as
Co-Chief Executive Officer. 14




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SIGNATURES
  SHOPKO STORES, INC. (Registrant)Date: December 15, 2005
    
    By:
    
    /s/ Brian W. BenderBrian W. BenderSenior Vice President,
Chief Financial OfficerCo-Chief Executive Officer*(Duly Authorized
Officer of Registrant and Principal Financial Officer)
  *
    
    The office of Chief Executive Officer is comprised of three executive officers, each serving as Co-Chief Executive Officer. 15




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EXHIBIT INDEX
SHOPKO STORES, INC.
10-Q REPORT
 ExhibitNumber
    
    Exhibit31.1
    
    Certification of Brian W. Bender, Senior Vice President, Chief Financial
Officer, Co-Chief Executive Officer*, pursuant to Rule 13a-14(a) under the
Securities Exchange Act of 1934, as amended.31.2
    
    Certification of Michael J. Hopkins, President, Pamida Division, Co-Chief
Executive Officer*, pursuant to Rule 13a-14(a) under the Securities Exchange Act
of 1934, as amended.31.3
    
    Certification of Paul G. White, Senior Vice President, Chief Merchandising
Officer, Co-Chief Executive Officer*, pursuant to Rule 13a-14(a) under the
Securities Exchange Act of 1934, as amended.32.1
    
    Statement of Brian W. Bender, Senior Vice President, Chief Financial Officer,
Co-Chief Executive Officer*, pursuant to 18 U.S.C. ss. 1350.32.2
    
    Statement of Michael J. Hopkins, President, Pamida Division, Co-Chief Executive Officer*,
pursuant to 18 U.S.C. ss. 1350.32.3
    
    Statement of Paul G. White, Senior Vice President,
Chief Merchandising Officer, Co-Chief Executive Officer*, pursuant to 18
U.S.C. ss. 1350.
 
 *
    
    The office of Chief Executive Officer is comprised of three executive officers, each serving as
Co-Chief Executive Officer. 16