Date: 201705
Local time of day: 1801-2400
Location: SMO.Tower, CA
Flight conditions: Marginal
Light: Daylight
Aircraft: Light Transport; Low Wing; 2 Turboprop Eng
Operator: Fractional
Operating under: Part 135
Flight plan: IFR
Mission: Passenger
Flight phase: Final Approach
Airspace: Class D SMO
ATC / advisory: Tower SMO
Second aircraft: Helicopter
Reporter organization: Government
Reporter function: Local
Reporter qualification: Air Traffic Control Fully Certified
Second reporter function: Pilot Flying; Captain
Anomaly: ATC Issue All Types; Conflict Airborne Conflict; Deviation / Discrepancy - Procedural Published Material / Policy; Deviation / Discrepancy - Procedural Clearance; Inflight Event / Encounter Weather / Turbulence
Detector: Person Flight Crew
When detected: In-flight
Result: Air Traffic Control Provided Assistance; Flight Crew Executed Go Around / Missed Approach; Flight Crew Took Evasive Action
Contributing factors: Human Factors; Weather; Procedure
Primary problem: Weather

Narrative: I had been on Local for about an hour. During that time; weather had changed rapidly from good VFR to low IFR as a low overcast marine layer moved in quickly. It was still reported clear to the east of the field; and I could still see the RWY 21 final from the tower. Within the few minutes leading up to this event; GC/FD and the CIC had generated a special observation that showed the airport IFR and passed it to concerned parties. Aircraft Y exited LAX airspace and requested a transition northbound; in VFR conditions; via the I-405 freeway; which intersects the RWY 21 centerline at about a 3/4 mi final. That aircraft was at 1300 ft. Around the same time; I received the hand off on an arrival; Aircraft X. Scratch pad coordination at the time of the hand off showed this aircraft assigned 'V21' (visual approach); but that would not have been appropriate with the newest weather observation. This coordination notation was later removed; indicating that the aircraft would arrive on the VOR-A approach. I used the STARS PTL (Predicted Track Line) feature (vector lines) to determine that Aircraft Y would get across the RWY 21 centerline in time; and I advised Aircraft Y that they would be crossing my final in advance of an arriving jet.Aircraft X subsequently checked on late; high; and with faster ground speed than I would normally anticipate at that stage. Step down altitude at WURUD is 1540 ft (a 3 mi final); but I recall Aircraft X crossed that point above 3000. I advised Aircraft X of the traffic (now 1/2 mi south of the centerline at 1300 and heading northbound) and issued landing clearance. Just afterward; I observed Aircraft Y passing the extended centerline; as Aircraft X was on a 2 mi final; also noting that they had arrested their descent at 1900 ft. I advised Aircraft X that their traffic was clear of final. On a 1 mile final; Aircraft X reported missed approach; still at 1900 ft and passing 1 mile south of the diverging traffic at 1300 ft. I issued missed approach instructions in accordance with the SCT LOA and performed required coordination. I switched Aircraft X to SCT Malibu sector. Before going over; the pilot informed me he had received an RA with the traffic.Aircraft X returned later and landed via the RNAV GPS 21 approach. I asked the pilot for some more information about the RA situation. I had guessed; and the pilot confirmed; that they were unexpectedly 'dumped' on the VOR-A approach. The pilots had briefed and were expecting the RNAV GPS 21 approach. Per local procedures; SMO ATIS should advertise both the VOR-A and RNAV GPS 21 approaches under these conditions. SCT Burbank area may issue either approach. I did not record or listen to the ATIS at the time because that is not a LC responsibility.I would not have approved Aircraft Y's I-405 transition with an aircraft arriving RWY 21 on [a] day where weather was not a consideration. However; this was a complex decision in that Aircraft Y had a need to maintain VFR east of the cloud layer. My judgment was correct that this aircraft would pass the centerline in advance of the arriving jet. Plus; I realized that Aircraft X would be out of position somehow; but I admit I did not know what the pilot's actions would be. Aircraft X's higher-than-anticipated ground speed and trajectory ended up reducing the separation. Ideally; Aircraft X would have been permitted to fly a stable approach and would have passed well beneath and behind the traffic; but the actual situation generated a TCAS RA because the device projected the aircraft descending on top of the traffic.I think the important lessons here are:1. Knowingly anticipating that an aircraft will have an unpredictable/unusual flight path should be a case for more positive separation. I could have asked Aircraft Y to fly eastbound until Aircraft X was in sight as weather would not have been a factor to the east. My Plan A (with Aircraft Y expeditiously crossing final) was very conditional; I realize.2. SCT's handling of the flight; Aircraft X was never in a position to land and a missed approach/go-around was likely regardless of the crossing traffic. This underscores the importance of adequate vectoring to allow an aircraft to fly a stable approach. Also at issue was possible mis-coordination or miscommunication regarding the approach to be flown by the Aircraft X crew. The weather changed very rapidly; but I believe our tower team made every attempt to provide the latest information to the arrival controller.The RNAV GPS 21 approach has been commissioned for [a short period] at the time of writing. It's hard for me to say what happened on that end; but I suppose the pilots may have briefed the RNAV approach as it would be preferred in general (LPV minimums); but the arrival controller may not have had the comfort and familiarity with that approach to issue it on very short notice.


Second narrative: On arrival into SMO; ATIS reported Marginal VFR and all approaches were available. We briefed the RNAV GPS RW 21 approach. ATC gave us direct DARTS; descend and maintain 4000. Outside of MIPTE; ATC said 'Cleared for the VOR A Approach'; we were shocked and wondered why we were assigned this approach. Altitude was approximately 1800 feet. I looked outside and noticed crossing traffic; we then executed a missed approach.There was heavy saturation regarding communication. With different approaches and traffic; we executed a No-Fault Missed Approach. During the missed approach; I then requested for the RNAV GPS RWY 21 approach and landed.


Synopsis: SMO Tower Controller and inbound jet pilot reported an airborne conflict between a jet arrival and a helicopter transitioning the area when weather deteriorated.