Temporarily he became a HM Slave, but he's nice and cosy in his box now. Being red means virtually nothing; everyone gets a Shiny Gyarados, which sort of defies the point if you think about it.
I've always had a bit of a beef with Gyarados. The whole Magikarp/Gyarados thing is a bit of a joke. Even though Gyarados is strong, by using Exp. Share or switching out your Magikarp it has no Effort Points, so it is a lot weaker than it could be. No, I've never really wanted a Gyarados in my team.