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The School of Life, also known as the School of Hard Knocks, is a school that John does not like at all, not that he really enjoys any other school he's ever been to.
It's at this School that he's learned that he has to do whatever it takes to survive and flourish in this life, but it's also where he learns that, if he stays with the X-Men (Bobby), he'll never reach his full potential, despite what they (Bobby) promises him.
So when he gets into the helicopter with Magneto and Mystique, he's only doing the right thing for himself and learning another lesson in the school of life; one that's painful and makes him turn back to see the heartbreak in Bobby's oh so blue eyes, and he falters for a moment, wondering if he's made the right choice, but then the helicopter is in the air and he has no choice now.