In a recent interview here: http://radish.hosted.doosh.net/stein...es/000027.html
the creator, Bob Dinnerman, said the following:
Ah yes, the 'infamous' last mission of F/A-18 Interceptor... As far as what I believe I did, the destruction of all enemy aircraft plus the enemy sub and a successful return to base should do it. I must note though, that the enemy carrier sub never actually blows up even if it's deemed destroyed! However I'm admittedly a bit remiss on exactly what constitutes the carrier sub having been destroyed, that is, perhaps the minimum number of cannon or missile hits on it, etc. I apologize for my brain lapse on this detail from 15 years ago! Another detail that I'm curious to know is if after one elects to and successfully lands on the carrier sub and gets rearmed/refueled, can he/she resume the mission and blast away at the carrier some more?! Some day I should find and dig up the code, go through it and verify what conditions are required to complete that mission. Again, my humble apologies. A footnote: Maybe the elusiveness to being able to complete this mission (though unintentional) has contributed to the game?s lure??
I completed the game many years ago and I seem to recall that a full load of missiles won't do the trick - you have to land and rearm and fire some more missiles at the sub. Which, by the way, can be a little tricky because you can't lock your missiles onto it. I think I had some success with attacking from high in the sky and then diving towards the sub while using the zoom feature to make sure that my aim was correct. Remember, that with a little practice, you can also land on the sub and rearm instead of returning all the way back to your own carrier. The other day I completed the first five missions in WinUAE and I will try to complete the last one for a second time whenever I feel like some serious trial and error-workout!
EDIT: And yes, it is the subcarrier in the upper left that you have to destroy. The only other carrier on the map, is the one you're taking off from. Not much sense in blowing that one up...