By the power of truth, I, while living, have conquered the universe.
Definately Gravemind.
The opening revelation that the Flood has an actual central intelligence was awesome, I'm one of the few fans who can say I loved that Little Shop of Horrors reject in Halo 2 because his character was so ominous and dark, you can tell he's got his own motives from the beginning and is able to persuade John and Thel to work with him.
Then we come to the level; a botched attempt to assassinate Truth, a rescue mission, the Covenant's divided loyalties (Sangheili fighting the Jiralhanae), a frontal assault on the Mausoleum and then a closing cutscene which makes it look like all hope is lost. Tartarus has the Index, Miranda and Johnson; Mercy is dead, making Truth the de-facto Covenant leader and he's on his way to Earth in the Forerunner Dreadnaught.
It was very well made, I really felt like I wanted to fight for the Elites (to the point where I never actually killed any). The music was divine too, tragic tunes that got built up and exploded into Breaking Benjamin at the end.