A/N: I really wanted to write this, but I've only actually seen about four episodes of Chuck. So if it's a little short on detail, sorry. Please feel free to point out any glaring mistakes, though keep in mind that this assumes Bryce is still alive after Chuck Versus the Ring.
He started by looking into Adler undercover, interestingly enough, as a con. The man was skilled and paranoid – there was no "in" through conventional means. But the mission was doomed from the start, and so it grew and changed and he continued to con. Then he goes to prison – in and out to conduct smaller missions on the side. Still, it's four years of his life that he's never going to get back.
From there to the FBI. It's fine, at first. He chafes at the anklet, but the knowledge that he can manipulate that irritation away is a much needed safety blanket. He works his angle and leaves the FBI to theirs. But then there's Peter. Peter, the man he admits to trusting. The only one, because to all others he is dead. But Peter doesn't know him. Not really. The man Peter knows is Neal Caffrey, and he's only about as real as Nick Halden.
Then there's Kate. She was never supposed to be caught up in this, but he loved her and now she's dead. It's his mistake, his guilt. Peter, when he stopped him from shooting Fowler, didn't understand. He couldn't, because Neal Caffrey may not be a killer, but Neal Caffrey is a lie.
When it's all over, and Adler's goal is stopped (the fractal code was never so benign as he'd told Peter) he feels regret. It's not the first time he's regretted a mission (Chuck and Sarah come to mind), and it won't be the last, but never so much as now. So he slides a letter into Peter's desk and prepares to be pulled out. A false undercover mission, a blank bullet, and a packet of his own blood – drawn over the course of a week. For his entire team to witness, Neal is shot in the chest. He's put into an ambulance, sits up, and listens to a CIA agent clinically report his death to one of his only friends in the world.
Peter will eventually find his letter, but it's only two words and a false name.
"I'm sorry," he repeats aloud, soft enough to not be heard. The agent snaps his phone shut and looks at him. She doesn't smile. There's no warmth in her words. So he feels cold when the agent finally says,
"Welcome back, Agent Larkin."