Negan is the newest threat in the world of The Walking Dead and he might be the most insurmountable so far. There doesn't seem to be anywhere Negan's control doesn't reach, and he's cheerful about exacting revenge on those who cross him. Negan functions on a kind of dangerous check and balances morality system that might be just as difficult to overcome as it is to live with. However, while Negan's journey on the show is just getting started, his fate has been sealed in the comics for a little while now. There's no guarantee that his story will play out the same exact way, but the comics are certainly a good guide. So what happens to Negan in The Walking Dead comics?
Negan makes an impact immediately in the comics when he kills Glenn with his barbed-wire-wrapped baseball bat, Lucille, but the big cliffhanger of Season 6 was just whose life Negan took. That might be a big hint when it comes to determining just how much the show will deviate from or elaborate on Negan's story in the comics. So if he does kill Glenn, then odds are the show will be mostly true to its origins. It should come as no surprise that Negan and his people constantly bump heads with Rick and his crew, and the resultant bloodshed ends the lives of more than a few characters.
After killing Glenn, Negan takes his group, "the Saviors," to Alexandria so that they can pillage their supplies. However, he ends up leaving with more than some snacks and bullets; Carl hides in Negan's truck and jumps at the first opportunity to take out a bunch of his people. Apparently Negan finds this charming, because he takes Carl under his wing and shows him the ropes of the Sanctuary, Negan's compound. Negan and Carl go on to form a strange bond with each other, which I'm sure Rick loves. (Not.)
There are a few more scuffles between the groups before they decide to partake in "All Out War," and it's not of the West Side Story variety. There's gunfire, walls collapsing, zombie attacks, grenades – everything goes to hell in a handbasket, to put it mildly. At the end of one fight, Rick manages to slash Negan's throat, though this doesn't kill him. Instead it incapacitates him enough that Rick can lock Negan up in a basement, where he's kept for two years. Negan eventually manages to escape, but that's the last anyone has seen of him in the comics.
Keeping Negan in captivity instead of outright killing him ties into many of the moral quandaries the show has raised, particularly in its most recent season. There has also been a lot made on the show of the fact that Morgan built a cage much like the one he was kept in years ago with the possible intention of reforming someone in the same way. From the sounds of things, that cage could very well have Negan's name on it.