Bob is just a hired gun who could easily find work elsewhere, so he feels no obligation to risk his life for Damien's lost cause.
Bob only works for Damien because he's holding his family hostage and will kill them if Bob doesn't do what he says. But Bob just found out a way to rescue them.
Bob was promised that if he helped Damien take over the world, he'd be his second in command and rule the world with him only to realize Damien isn't going to keep his promise and/or is going to lose no matter what.
Bob is a Chaotic EvilPsycho for HireNietzsche Wannabe who thinks rules are meaningless abritrary concepts we enforce to make ourselves feel more significant than we actually are. While Damien is Lawful Evil and has no problem bossing him around. Bob just figured working for him just isn't fun anymore.
Inverted: Bob, Jesse's arch-rival, joins Damien's army just in time to fight Jesse.
Subverted: Damien catches Bob trying to escape and drags him back to his post.
Double Subverted: Once Damien is distracted fighting Jesse, Bob manages to escape successfully.
Bob keeps a packed suitcase by the back door, ready to run at any given moment.
Bob puts up with all manner of humiliations while working for Damien; however, the last straw comes when Damien cancels Casual Friday (or makes him work overtime without extra pay).
Zig Zagged: Bob flees before the fight starts, but then changes his mind and comes back. However, when he sees Jesse single-handedly wiping out the rest of Damien's army, he turns around and runs again.
Averted: Bob does not attempt to run from the battle.
Enforced: "We want to bring Bob back for the sequel. Let's keep him away from the final battle to explain how he survived."
Lampshaded: "I can guess how this fight's gonna turn out, and I want no part of it!"
Jesse manages to convince Bob to walk away without a fight.
Jesse operates as a Terror Hero to inspire this reaction.
Bob 'gives up' in order to surprise attack Damien.
Bob gives up and pulls a Mook-Face Turn... but it turns out that he's still loyal to Damien, because Bob and Damien both know how forgiving the heroes are.
Defied: Damien equips Bob with an Explosive Leash to prevent him from going AWOL.
Discussed: "So you're working for Damien, huh? Got an escape route planned yet?"
Conversed: "If Bob has any sense, he'll get outta there while he still can."
Bob's desertion is indicative of Damien's shortcomings as a leader, as he is unable to inspire loyalty in his followers.
Bob becomes a target for revenge amongst those who remained loyal to Damien.
Reconstructed: Bob up and ran because he realized how just plain evil Damien was and didn't want to put up with his bullshit anymore. He later becomes a valuable companion to Jesse.
Played For Laughs: Damien makes a grandiose speech about fighting Jesse to the last man, then turns around just in time to see Bob slam the exit door behind him.
Bob's exit comes at a crucial moment in the battle, leaving Damien at Jesse's mercy.
Bob left because Damien does all the horrible crap he does just because he can. Since even Bob has standards, the latter ran away from the battle. Which is bad for Damien, because Bob was one of his best soldiers.
Bob and Damien used to be good friends. Bob's decision to quit comes at the end of a great deal of internal conflict for him.