The Daily Show/WMG

Stephen Colbert killed and ate Jon Stewart, replacing him with a robot.
This happened some time before the launch of The Colbert Report, as Jon's ghost appears in the Colbert Report studio (the old Daily Show studio) during a seance in a very early episode. It's the reason for the Toss in late 2005 which revolves entirely around 'cranberry sauce' (see 'Paul Is Dead'). Assuming it happened some time in early 2005, this also explains Stephen's claims to have eaten a panda in the mid-2005 "Bloggers" sketch: attempts to throw the bloggers off the scent. Also note the voicemails left by Stephen for Anthony Pellicano in 1999, revealed on the Report, in which he repeatedly arranges and cancels Jon's assassination.

The need for the robot replacement is explained in the episode where he eats Bobby the stage manager: "[Colbert], you can't eat another co-worker! They're still looking for [previous host of TDS] Craig Kilborn." Also note that Jon (the robot) never appears on the Colbert Report without being tricked or otherwise coerced - until the feud with Conan O'Brien in early 2008, during which the ghost of the real Jon possessed the robot in order to save Stephen. This is why Stephen was so shocked to see him.

This explanation also accounts for various strange comments made by Stephen in interviews, most notably when he told Bill O'Reilly that he and Jon "don't talk". They don't. Jon's dead.
 * Stephen's fear of robots (as seen in multiple Threatdowns) is based on a fear that someone will find out what he did.

Kristen Schaal is a horse.
Kristen Schaal is a horse, Kristen Schaal is a horse! Look at her dance and look at her go! Look at her dance like a horse! Kristen Schaal is a horse! Kristen Schaal is a horse, Kristen Schaal is a horse! Look at her dance and look at her go! Look at her dance like a horse! Kristen Schaal is a horse, Kristen Schaal is a horse! Look at her dance and look at her go! Look at her dance like a horse! Kristen Schaal is a horse! Kristen Schaal is a horse, Kristen Schaal is a horse! Look at her dance and look at her go! Look at her dance like a horse! Kristen Schaal is a horse, Kristen Schaal is a horse! Look at her dance and look at her go! Look at her dance like a horse! Kristen Schaal is a horse! Kristen Schaal is a horse, Kristen Schaal is a horse! Look at her dance and look at her go! Look at her dance like a horse! Kristen Schaal is a horse, Kristen Schaal is a horse! Look at her dance and look at her go! Look at her dance like a horse! Kristen Schaal is a horse! Kristen Schaal is a horse, Kristen Schaal is a horse! Look at her dance and look at her go! Look at her dance like a horse! Kristen Schaal is a horse, Kristen Schaal is a horse! Look at her dance and look at her go! Look at her dance like a horse! Kristen Schaal is a horse! Kristen Schaal is a horse, Kristen Schaal is a horse! Look at her dance and look at her go! Look at her dance like a horse!
 * And that's how a bill becomes a law!
 * The internet is weird.
 * You're just now figuring this out?
 * The real life Mel from FOTC, ladies and gentleman.
 * Au contraire, for she is a triceratops.

Everything Stephen Colbert says about himself in the following clip is true
http://www.thedailyshow.com/video/index.jhtml?videoId=128895&title=Bloggers
 * So Stephen Colbert is actually Hitler's grandson.

Chuck Bartowski is Jon Stewart's son.
Seriously look at them.
 * And Jack Thompson (seen being Jack Thompson) is his father.
 * And Jack Thompson (seen being Jack Thompson) is his father.
 * And Jack Thompson (seen being Jack Thompson) is his father.

Jon Stewart is Jack Thompson... and a Master of the Timey Wimey Ball.
Seriously... Jack Thompson gets really, really old (even older than he is now) and suddenly realizes all of his "crusades" against videogames and "dangerous programming" are ill-advised and detrimental to freedom (and fun). So he replaces himself with a clone, goes back in time as a much better-looking version of himself to be an activist for free speech and freedom of the press. His original goal was to at least cancel out the effect his original fear-mongering had. But of course, now that he's spouting logic and reason, he's far more respected, successful and decorated than he ever could have hoped to be. He learned his lesson... and he makes $11 million a year. This might explain why Jon Stewart never mentions Jack Thompson on his show.
 * Well, that's PROBABLY because if he did, a time paradox would wipe them both from existence. While Thompson's eradication would be And the Fandom Rejoiced, Jon's would be...well, what's the trope name for the opposite?
 * deciojeR modnaF ehT dnA?
 * So Jack Thompson would go from the far-left Fascistic moron to the articulate center-left comedian and pundit? Quite excellent.

Either in the comics or real life, Jon will receive a Green Lantern Ring
This practically writes itself, people.
 * That makes an odd amount of sense. That would make Obama a Blue Lanter, and the Bush administration Yellow Lanterns because of their constant fear-mongering (ironically, the same as the terrorists). Throw in Stephen as a Red Lantern, maybe, and you've got yourself a nice story.
 * Speaking as a person who does not read comics, ever, I would read this comic.
 * Stephen Colbert could only be a Red, White and Blue Lantern!
 * Technically, that would be white, with greater parts Red and Blue than the other colors. White Light is an emotional mix, not a distinct emotion unto itself.
 * Given that during the rally to restore sanity and/or FEAR, not to mention he is Jon Stewart's Arch Enemy, he's probably a Sinestro Corp (yellow lantern) member.
 * Someone write this, please! I would read that in a heartbeat.

Jon is a Kamen Rider.
He's recently stated that his goatee's name is Phillip, and that together, they fight crime. Sound familiar?

In the wake of this, Jon Stewart will be forcibly welcomed into the world of political punditry, whether he likes it or not.
Bill O'Reilly, Chris Matthews, Glenn Beck, Keith Olbermann, Rachel Maddow, Sean Hannity et al will crash his show, simultaneously chanting "ONE OF US! ONE OF US! ONE OF US! Stewart will then soil himself.