Mr Sprout over at the new Halo Wars fansite, Halo Wars Central, was able to get an interview with Dispraiser, the lead of Slipstream Productions that was working on the Halo-themed Halogen mod for Command & Conquer Generals: Zero Hour. Shortly before the announcement of Halo Wars for the Xbox 360 at the X06 event in Barcelona, Spain, Bungie contacted the Slipstream team with word that Microsoft's legal department wanted the team to stop working on their mod as they considered it an infringement of Microsoft's intellectual property, the Halo universe.
However, the team has not stopped working on the mod-- it just isn't Halo themed any more:
Well, it'd take the mystery out of it if I just said what our next project is, but a lot of our fans have found the secret message (rather crudely hidden) on our old homepage. I think if I just said what we were up to it'd take a lot of the fun out of making everybody find that message... But lemme just say, if you liked Halogen for more than just the Halo name, and you saw the work we put into our creations, and our faith to our motto (Semper Qualitas), then let me say that you won't be dissapointed.
For those still unclear on what actually happened with the cancellation of Halogen, read the interview.