Film about a kid who lives in a ufo and time flies.?

This film is about a kid who gets on an intelligent ship with a personality and travels all over the place. One day he is brought back to his house and his family is 10 or 15 years older. As he leaves his family again, the military abducts them and they are able to escape and the ship at one point flies over a wetland or swamp and the ocean and goes underwater. That's all I know for now, thank you.