The pilot of the RF-4 came through Randolph T-38 PIT back around '94 or '95. I was an IP there, and he gave his version of the story to us while showing us the Tomcat video. I don't remember enough details as clearly as I should, but needless to say, his version is very harsh on the Tomcat pilot (but not the RIO). He was tracked for a long time, and the pilot claims he thought it was an Iranian F-4. If I recall right, he said the Tomcat pilot's father did an air-to-air kill years prior.
Anyways, I don't know where he got the info, but since it had been 7 years since the incident, he had had time to get the scoop on what happened.
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IIRC, the Alaska Eagle blue-on-blue was with 2 Eagles that were on alert. I guess they get to occasionally get to launch for some flight time, and that's when the near-frat took place. The shooter was a 1Lt.