Yeah, I hate to agree with Hades here, but he doesn't fly off, he just vanishes, like he usually does. It's been speculated though, that either he has levitation abilities, through an actual levetation ability, or through his telekeisis as Tale said, because the woman with super hearing said soemthing like "I didn't hear your footsteps" and Sylar was all like "That's because there weren't any" or soemthing.
I don't really remember a hooded guy, I remember Sylar in a hat, and maybe with a hood over his hat, but I think that this hooded guy from the first seasn that you are all talking about was just Sylar.