The Tonight Show/WMG

Conan's "Puppies Dressed As _______" segments were a Take That to Jay Leno...
...who has made no secret of his distaste for dressing animals up in costumes, mentioning it in approximately one out of every three Headlines segments ever.

NBC's whole fiasco of screwing with their late-night schedule was one big attempt at trying to prove there's No Such Thing As Bad Publicity.
Sadly, NBC used Insane Troll Logic to help improve ratings by causing such a controversial move by kicking Conan off The Tonight Show, canning Jay's own show, and putting Jay back on Tonight.

The Tonight Show with Conan O'Brien's ratings were starting to increase after this stunt was pulled, so by screwing Conan out of Tonight and getting Jay a load of bad PR, they're using those two as pawns for a publicity stunt.
 * If NBC were smart in this scenario, then they would have used Reverse Psychology to ensure the public supports the guy they want to get the show. But this is NBC.
 * During the final weeks of The Jay Leno Show, Jay didn't have an agent. And when he was on Tonight the first time during the writers' strike, he thought he was still keeping the strike despite returning to the show because he was writing all his material. (Ironically, those were some of the better monologues of the late 2000s.) He could easily be a pawn here.

Jay might have been able to protect his reputation if The Jay Leno Show never happened, but NBC would've screwed Conan over anyway.
If The Jay Leno Show had never happened and Jay just got out of the talk show business altogether (or at least until his non-compete clause ran out), then people wouldn't have blamed him for destroying the network, and they wouldn't have resented NBC giving The Tonight Show back to him as much...

But Conan would've still lost Tonight. The ratings for Conan's run on the show weren't bad, and the ratings for The Jay Leno Show were not that much better. Unless Conan's ratings substantially improved over the last years of Leno's Tonight, then NBC would've still kicked Conan off Tonight and replaced him.

The entire late-night fiasco is the fault of the head of NBC...
...and he wears a gingham dress and carries around a penguin puppet called Mr. Flibble. It's obvious.

The network doesn't know what to do with the show now that Kevin Eubanks has left.
The interplay with Eubanks was the last funny thing about Leno's monologues, and it's been some time since Eubanks' last show. The Retool going on behind the scenes must be frantic. Zucker's gonna reeeeally wish he'd stuck with Conan...
 * Zucker did whatever Mr. Flibble tells him to. (See above.) Well, until the Comcast merger — the cable company's first move was to fire Zucker, specifically for causing this whole mess.
 * Situation resolved, sort of. They've replaced Eubanks with Rickey Minor. Clearly, NBC is hoping to use The Tonight Show to destroy American Idol.

Conan went into a coma when he hit his head.
Everything that's happened ever since is his coma fantasy.