The Magus eventually catches up with him, and Warlock can't just keep running.

The Magus eventually catches up with him, and Warlock can't just keep running. The fight goes through Limbo and into space, with the Magus infecting what he touches and threatening far more than his own son. By New Mutants #50, he's powerful enough that the team needs to work together just to have a chance. Doug and Warlock solve it by altering his genetic code and turning him into an infant. They don't outmuscle him. They use what they can understand about his body while Xavier helps coordinate everybody else. Warlock tells Xavier that he's his father in spirit. That's a pretty clear statement from somebody whose actual father has been trying to make him participate in a death match. The school has given him something he couldn't get at home: people who want him alive without demanding that he prove himself by killing somebody. It also gives him people to lose, which becomes a much bigger part of his story than he could have understood when he arrived.