My theory:
On a sunny morning in late 2007, a bunch of Navy SEALS burst into Bungie's secret headquarters. There, they interrogated multiple employees for unknown reasons, then stole a torn piece of paper which had 'Halo belongz 2 meh!' written on it. They then planted a microchip in Stosh's brain, forcing him to ruin everything or he would implode. Then they planted microchips in every other employee's brain forcing them to blame Stosh or they would implode.
The SEALS then returned to Microsoft with the torn piece of paper. With a simple "Excellent", Bill Gates formed 343i and gave them the torn note. With Halo in 343's hands, they returned to Bungie and gave the letter back, claiming it was all a joke. What Bungie didn't know was that the note was a magnificent forgery, and the real note still belonged to 343i. They then decided to wait until Bungie made a game that would disappoint the community (Halo: Reach) so that the world hated Bungie (That part didn't work though).
After Reach's release, 343i revealed that they still had the real Halo rights. They then laughed a chilling laugh, and promised they would ruin the franchise with 3 horrifying sequels which would destroy the universe. The end.
[Edited on 04.25.2012 2:56 AM PDT]