Super King Air 200
Air Traffic Control Fully Certified
Air Traffic Control Time Certified In Pos 1 (yrs) 11
Communication Breakdown
ATC Issue All Types; Airspace Violation All Types; Conflict NMAC; Deviation - Track / Heading All Types; Deviation / Discrepancy - Procedural Published Material / Policy; Deviation / Discrepancy - Procedural Clearance
Air Traffic Control Issued Advisory / Alert; Flight Crew Returned To Clearance
Chart Or Publication; Airport; Procedure
I was on LC1 with multiple aircraft in the south patter when Aircraft X checked in from the west requesting left traffic for runway 28L. LC2 was working runway 28R and the north pattern. I sequenced the pilot to follow Aircraft A on base turning final and also told the pilot about Aircraft Y on final for the parallel runway. Aircraft X reported the Cessna to follow in sight; so I cleared him to land. Aircraft X turned too early and I informed him that spacing between him and the Cessna was not going to work out. The pilot then says he's going to make a 360 and took action without realizing there is other traffic in his vicinity. I quickly informed him of traffic and he responded that he had traffic in sight. He made a right turn directly towards Aircraft Y who was on final for the parallel runway. Aircraft Y had to take evasive action to avoid Aircraft X. I told Aircraft X to go around and offset right of the runway and told him about traffic in the north pattern. He reported a Cessna in sight and began a turn to the right downwind quickly overtaking the Cessna on downwind. I instructed  Aircraft X to extend downwind to follow traffic on final. He reported the Cessna to follow in sight (Aircraft B). Again; he turned base too early and I had to send the Cessna around to get Aircraft X to land.The pilot of Aircraft X may have misjudged the spacing required to follow aircraft that are much slower than a BE20. The pilot took action on his own without being aware of his surroundings. He should have verified with ATC before making any turns.
As Aircraft X approached the MYF D airspace; crew noted there were approx 10 TCAS contacts within the D airspace.  Crew discussed flying slow as possible to help see/avoid. Aircraft X was cleared into MYF class D by tower.  We were cleared to join left downwind for Runway 28 Left.  Just prior to downwind we lowered gear and flaps to fly as slow as possible (approx 120K IAS).  Approaching abeam landing point tower told us to extend downwind and to take interval on an aircraft already on final to 28 Left.  Flying Pilot saw aircraft on final and turned to take interval.  We were also told there was an aircraft on long final to 28 Right.  After turning to take interval on 28 Left traffic; Tower called and said something that made pilot flying think he was taking interval on the wrong aircraft...that there was another aircraft on final to 28 left.  Pilot rolled toward level to look for other traffic.  Doing so put us close to runway 28 Right final course.  Pilot called tower and began to execute a right 180 to clear the final for both parallel runways.  In the turn; pilot saw the aircraft that was making approach to Runway 28 Right and executed a level nose down maneuver to allow aircraft to fly over and laterally to the right.  Tower told us the 28 Right aircraft flew over us.  Aircraft X landed 28 Left and was told to contact tower for possible pilot deviation.Lesson learned.  Tower told Aircraft X that he was flying 'fast' making sequence difficult with GA aircraft and that 28R is preferred runway for Aircraft X size/speed aircraft.  Aircraft X reported that we requested 28L ONLY because we thought it would be easier for ATC not the crew.  Given the traffic saturation it seemed a direct entry to left downwind to 28L would be preferable than overflying field to entering right downwind for 28R.Aircraft X reported to tower that they were flying as slow as possible and that if tower had preference to which runway they could have communicated that to Aircraft X.  Also; tower informed Aircraft X that the two parallel runways use different control tower frequencies.  Aircraft X did not have as good of SA on runway 28R since they couldn't hear the transmissions to/from that aircraft. ForeFlight EFB is used by the Aircraft X company pilots.  ForeFlight lists both tower freqs but list one as 'secondary' not as for other runway.  MYF AFD also does not say that there are different tower frequencies with one being for 28L and the other for 28R.Tower is probably hesitant to 'counter' which of the parallel runways the pilot has requested to land.  However when a non-local aircraft if flying into an unfamiliar airport which is congested with many different types of aircraft. It would be helpful if Tower would make suggestions for appropriate runways.  Pilot would still have prerogatives to stay with what was requested.  AFD should have notes that indicate two different frequencies are used SIMULTANEOUSLY for the airport.See and avoid is still critical in VMC conditions.  Just because Tower or Approach gives an aircraft a clearance to land...or vector if IFR the pilot still need to keep a look out to avoid collisions.
Air Traffic Controller and BE200 Captain reported confusing instructions which created an airborne conflict resulted in pilot reporting a NMAC.