As far as I’ve been able to find out the joke is just that, only a joke they made up for the show to tie the two stars together. That was actually the real Tom Brady and Jay Leno that did the voices for that episode.
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What is the story behind the Family Guy joke about Tom Brady & Jay Leno?
Jay Leno is really the “Midnight Rapist” he was trying to ɾąքҽ Brady and steal his superbowl ring. Of course, Brady has his counter ɾąքҽ machine which is Belicнιcκ with a Louisville Slugger.