Second track of Disk 2 of the Halo 3 Soundtrack.

Black Tower (0:00 to 2:22) plays during the battle at the third tower. The part at 1:10 and up plays during the cutscene that plays after deactivating the third tower, and continues as the Flood-infested High Charity appears, right through the part where the Flood dispersal pod crashes through the Shadow of Intent, and slams into your tower. Also, if you play this part of the track in reverse, there is yet another secret message, this time from a source, being the Gravemind:
"Eyes from death's dream kingdom.
appear as sunlight on a broken column.
There, in death's other kingdom walking alone,
trembling lips from prayers to broken stone."

Heroes Will Fall (2:23 to 6:05) plays during the cutscene where Miranda crashes her Pelican into the control room to save Johnson from Truth and stop the latter from activating the Halos. 3:35 right through to 4:36 plays during the part where Truth kills Miranda, and where he forces the weakened Johnson to activate Halo. From 4:37 onwards is the rest of the cutscene. It is a remake of Rue and Woe from the High Charity Suite of the Halo 2 Soundtrack.