If you took long enough on the final GDI mission you get a cutscene during the mission with Granger telling you about the Liquid T bomb and that you shouldn't use it, 'cos it'll kill loads of people. Boyle interrupts and tells you you'll be a hero if you use it. Mission continues and you can now launch a Liquid Tiberium Bomb to get the bad ending (25 million dead, mass fallout, but you get to be head of the army. Granger resigns)

All the endings are canon in this game, just as with Tiberian Sun: Firestorm and Generals (Each Generals campaign lead into the next)

One tower is completed thanks to Nod's protection, the tower which the Foreman (Scrin player) escapes back to the central hub through, and the one which the GDI think is inert. The expansion for C&C3 is set for a spring 2008 release, and will be addressing what happens after Tiberian Wars endings, so fear not! We shall find what happens to Kane and his inner circle soon enough.