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if i was actively seeking excruciating mental pain and a lot of snotty crying in theaters, i would have recommended they make stephen, while making the spell for people to forget peter, have an unusual bout of uncertain and stilted speech and say something along the lines of "he didn't make me promise to--but tony would have--wanted me to keep you... he wouldn't have wanted..." and for peter to smile bitterly and shrug a little and say "well. tony--i guess it doesn't really matter any more." everything else can stay and everything else goes as it does in canon.
but of course i am not actively seeking any more excruciating mental pain and snotty sobbing than the movie already gifted me