Nathan Drake is nice. Too damn nice for his own good. Almost too nice to be in the profession he's in. His trust is implicit, and he gives it too quickly and too easily, despite everything that Sully's taught him – always willing to believe the best about everyone, even when all the evidence points to the contrary. Sure, he'll lie and cheat and steal like nobody's business, but Sully can't count on both hands and feet the number of times that Nate's gotten into trouble because he believed something – or someone – only to be proven wrong, often in a near-fatal way.
This is especially true of his friends. Sully has no idea why the kid keeps hanging around Chloe Frazer. She's betrayed him once, twice, and she'd do it again in a heartbeat. She reminds him a little bit of Marlowe in her younger days; beautiful, vibrant, and entirely ruthless. Sully still can't think about Harry Flynn without getting irritated and just the slightest bit angry. Elena is one of the first people Nate has formed any kind of close relationship with and not had turn on him – Sully being the first.
So when Cutter turns on Nate in the cave, Sully is furious. As he hurries back through the gap in the wall, he can hear Nate arguing with the Brit. I don't want to fight you. I'm not going to hurt you. When he and Chloe burst back into the cave, Nate is on his back on the ground, being strangled by a man he trusted and still trying not to harm him. Sully gives Chloe approximately 5 seconds to try to talk Cutter down before he puts a gun on the man.
Cutter, listen to me. You are killing Nate. The older man's grip tightens on the trigger just as the Brit stumbles away, looking confused and frightened. Letting out a breath he hadn't realized he'd been holding, Sully holsters his gun in favor of helping Nate to his feet, of letting his protégé cling to him as he gulps down the air he'd been deprived of. Then he watches in disbelief (but he shouldn't have been surprised, because it always happens) as Nate brushes Cutter's apology off – we're even, it's fine, don't worry about me.
But Sully is not so willing to forgive. He has one good thing in his life, and he keeps coming far too close to losing it. Nathan Drake is a nice man. Victor Sullivan is not. There were some who would do well to remember that.
You weren't going to shoot me, were you?
Like a rabid dog.