What did Muir think was going to happen after he left McLean?

Let's look at the options the CIA got:

• Pursue him legally. Although he has certainly broken the law with his actions, the CIA cannot just admit that they got deceived by a single employee who invaded a (quasi) enemy country with a marine team just to enforce his own private goals. That would be quite embarrassing. I don't think the few bosses from the conference room can even tell it to the rest of the CIA.

• Secretly punish him financially. They are surely able to do this, but what should they take, since he lost his whole money for this job. On the other hand the government didn't lose any money.

• Secretly kill him. They won't do him any physical damage, they're just not the bunch of cliché evil-guys killing people for fun and are not depicted in that way in the movie either.

• Secretly imprison him. They could certainly do that, but again, they would have to keep this entirely secret, since as few people as possible outside of this small conference room should know about Muir's actions. Additionally I'm not sure if imprisoning him would really buy them anything.

So considering the fact that they cannot tell anybody, not even the rest of the government or the CIA, what Muir did, and the fact that Muir used his own money and is just a poor old man now, from a pragmatic point of view they neither have many possibilities to punish him nor a large motivation to do so. They may certainly observe him in order to get sure he doesn't talk about what he did, but why should he do so.

But in the end I'm not that sure the script writers really thought about this that largely. Usually the audience just doesn't think outside of the movie's limited time frame. Think of the mandatory romance in your favourite action or adventure movie, of course they will split afterwards since they just don't fit together, but they have to kiss at the end. In the same way Muir just has to drive away from the CIA in the last moment, no matter if they know where he lives and what he's done.

Don alder Howell's answer about Muir protecting Troy Folger may be based on a "deleted scene" from the DVD.

Folger meets Muir in a weird place which looks like a cafe in Egypt. As Folger is reviewing Muir's ops report he comes to a question that asks for an evaluation of Hadley's future threat. There Muir wrote "unknown". So Folger reads this, questioning it in a surprised way: "Possible threat... Unknown?!...I want to know what are we going to do about Hadley.".

Muir says "I'm done with Hadley!", meaning he doesn't want to mess with her. But Folger says "Nathan, if you don't deal with her, I will." Then Muir says kind of angrily "Yeah, why don't you fill a bus full of explosives and run her over?!" Based on that scene, Muir makes the deal to give Hadley to the Chinese. He didn't seem to want to, but it was better than leaving Folger to do something crazy.

So when Muir is asked the question whether he did it on his own, this deleted scene pops up as a remembrance -- both Folger and Muir remember it -- and Folger breathes relief when Muir only blames himself, instead of pointing at Folger for giving the order without a "finding."

Nathan Muir protected his Boss Troy when Nathan said that he worked alone in brokering the deal to trade Hadley for an imprisoned diplomat.

He was clearly protecting Troy and therefore he would be covered from any criminal issue

When we see Muir driving away from CiA at the end, he has exited on to Route 123 North. Then he drives less than a mile to exit for the GW Parkway. He appears to be headed towards Maryland via the GW Parkway which runs alongside the Potomac River. He was definitely not headed home. The GW Parkway hooks up with 495 just a short distance from CIA. The last shot shows Muir crossing the Cabin John Bridge aka The American Legion Bridge. More than likely after that he took I 270. I get a thrill out of this scene because in 1990 I drove my French boyfriend's 911 across that same bridge. And yes, I was going very fast. 120 mph.