TheWriterFantastic™
Explorer
Apparently, classic studio interference altered both films, not just the 2nd - originally, there was only one missile in the first film, with that almost hit the fault point where an unaware Lois Lane was coincidentally enjoying lunch at a taco stand. The Salkinds were losing their minds about Donner repeated going over budget and were worried about how much money they'd lose if Part I wasn't a hit, and the time rewind sequence had already been shot and cost a ton, so they ordered it tacked on to the end of Part I. Originally, the one nuclear missile would have been tossed into space by Superman at the end of Part I, with the explosion releasing the PZ criminals as a cliffhanger to rope people into coming back to watch Part II. When the studio forced the new ending, they had to add the 2nd missile and the metaphorical "train problem" (coincidentally or not also briefly including a train) to save the people of NJ, or the people of CA (including Lois).Sorry, you’re right. I haven’t seen it - where does the missile come from, is it from the first film?
Read the summary on Wikipedia - so he uses time travel again to reset the whole universe so presumably the prisoners remain in the Phantom Zone, which is interesting and also makes more sense than a memory wipe kiss.