My favourite part about the handshake at the end of Brand New Day is that Peter chooses it. It's not just a muscle memory thing that catches them both off guard - there's a pause just before Peter shifts his grip, and then the handshakes changes and the muscle memory kicks in.
We know Peter stays away from Ned and MJ because he thinks their lives will be safer, even better without him. But I wonder if there's also a part of him that dreads starting from scratch - if the spell truly can't be broken, reconnecting with Ned and MJ would be so painful. He lost everyone, and if they chose to leave him again, how would he cope? So he stays away and tells himself it's for the best, even while he yearns to be with them.
And I imagine that fear would have only grown after MJ admitted that she didn't love him!! How crushing to learn that the woman you've been pining for all these years has no memory of you at all? What if your best friend has also forgotten you forever?
But MJ sees this broken guy who has been alone for a long time, and thinks of her roommate and his search for Spider-Man, and she quietly prods Peter to come back into their lives. She invites him into the apartment and shows him that while Ned might not remember, he has been missing his best friend all these years. Then she gives Peter something that he didn't get with her: she gives him the chance to choose his loved ones. And eventually, Peter reaches out to shake Ned's hand.
