A/N The termination order on Chuck in the beginning of Season 2 was a typical example of a plot device created for dramatic effect that makes very little sense when examined up close. Both illegal and immoral, it really paints most of the characters in some very unpleasant colors, and unsurprisingly was used and dropped with as much speed as they could.
Lots of fanfic authors deal with this dilemma in a variety of ways, usually unsatisfying, at least to me. (I did two myself and I'm not entirely happy about either of them.) The most recent example, from Becoming, by Arya's Prayers, along with the stunningly good Chuck vs Pillow Talk, by AgentInWaiting, gave me the idea for this story. It's short, just my attempt to make sense of it all. The goal here was to present an interpretation of events that stayed canon, but allows our heroes to be heroes.
He used the Morgan Door, of course.
Chuck's room was dark, so he flashed a low-beam light to get his bearings, and spot potential booby-traps. He expected none, but the day he acted on his expectations instead of solid intel was the day he retired, probably feet first. As expected, he saw none, Bartowskis being clean freaks and all, and so he dropped the beam.
The light coming under the door was enough to get him there, and he paused, listening. He didn't want to be here, but he had his orders. Failure to comply would only get them all killed, and not as nicely. If it had to be done, he wanted it to be done nicely. Clean, quick, and painless. Save the nasty stuff for those who deserved it. Chuck should never see him coming.
He heard a voice. Who was Chuck talking to? This whole operation had been planned down to the last detail. He had some margin in it, but not for the usual stupid screwups that plagued most of their other operations, no matter how successfully they'd turned out. He raised his silenced pistol, and cracked open the door.
No one in view. He could hear Chuck talking, but he didn't seem to be talking to anyone. What was he doing, rehearsing? He rolled his eyes. Overthinking everything about his dinner with Walker, as usual. Life would be so much easier if one of these clueless idiots would just say something. Too bad tonight had to be the end of all their chances.
The phone in his pocket vibrated silently. Time for the next phase. With a dental mirror he checked the living room. Chuck stood by the table, forgetting to keep his back to the wall, again. Just as well, this time.
Someone knocked on the door, and he shrank back into the shadows, checking his watch. If that was Walker, she was a little early. She was supposed to find the body, that was the plan. Killing the kid in front of her was an avoidable cruelty, but as details went it was pretty negotiable. He tracked his target across the floor by sound, waiting for a clear shot. He'd only have a second before the door opened and spoiled everything.
His finger was squeezing the trigger when Sarah launched herself through the door, displacing his target and talking a mile a minute, not letting Chuck get a word in edgewise. A minor miracle. He listened as she talked, backing away from the scene of the almost-murder.
So the Cipher blew up, no surprise there. No new Intersect, so they still needed Bartowski. Time to go. They'd be going over to his home base soon, he had to look innocent.
As he crossed the courtyard he picked up his motion detector, aimed at the tunnel and linked to his phone, so he'd know when Walker arrived. In the apartment, he racked his gun and washed his hands, going to his surveillance gear. The lovebirds were still talking, no surprise there either, although for the life of him he didn't know why they should be so surprised.
The Cipher was easy enough to booby-trap, after all, just in case those Fulcrum traitors managed to get a hold of it again. Which, amazingly, they had. And they could be expected to gimmick it too, something crude, of course. So easily found, the guys looking for the gimmicks stopped looking, just a bit too soon.
It wouldn't have been a problem if someone hadn't been in a rush. Someone wanted Chuck dead pretty damn bad, after all, some traitorous, treacherous bastard, after all the moron had done for his country. Whoever it was would almost certainly pounce on the Cipher and use it, before it could get stolen again. Fifty-fifty who would get it, Beckman or Graham, but for the sake of his agency he hoped it was Graham, and it seems he was right. Never trusted that guy. Hopefully, with him gone Beckman would straighten out and fly right.
He smiled, and rewound the whole event, watching as his every step was captured, proof that he was on the job, ready to do his duty, until interrupted by an act of God.
Or an act of Casey.