Re: Heroes 3x25 "An Invisible Thread" Discuss and Grade (SEASON FINALE
As has been pointed out, all Sylar ever really wanted was to be, well, wanted. Living as Nathan, he'll get that.
Until they find out he's Sylar, then it's done. There's nothing inside Sylar to battle for possession of his body or identity. There is no Nathan, only a false mask. An inanimate object. It can't fight for anything. There's not going to be a battle. There's not going to be Nathan 2.0. There's nothing left to be Nathan 2.0. "Nathan" is a post hypnotic suggestion left by Matt. The person in Sylar's head doesn't exist. Once Sylar remembers, he's Sylar again 100 percent.
Maybe they'll build up to another incredibly disappointing, non existent fight between Peter and Sylar.

From which Sylar will escape, of course.
But you're missing the point. Psychologically speaking, there
is a Nathan. Regardless of how it was put there, or how fake you feel it is, there is still a personality there, and the more time it spends in control, the stronger it will get, the more it will develop, and the more it will want to stay in control. As long as the Sylar persona tries to push its way through, the Nathan personality will fight it for control.
For example; look at The Doctor, from the Doctor Who two-parter
Human Nature/Family of Blood -
[SPOILERS]; he used technology to implant a false personality into himself, a Human personality used to disguise his true self from some nasty aliens. This process also involved altering his DNA to appear Human too.
Even though the personality was fake, the longer it was in control, the more used to its life it got. It was unaware of what it really was, and thought it was a real person - John Smith, a man who had a life, had friends, collegues. A man who fell in love with a woman.
When it came time for John Smith to be changed back into The Doctor, the dominant Smith personality didn't want to go. He didn't want to die, he wanted to have a life with the woman he loved - he knew that could never happen if The Doctor's true personality returned.
In the end, the only reason he sacrificed himself was because if he hadn't, everyone would die, including the woman he loved.
Later, The Doctor said that some part of the John Smith personality did still exist somewhere inside him, but he knew it was a life he could never have.
So, as I said, regardless of how the Nathan persona got there, it isn't any less real than any other personality, and it will fight for its existance.