Soon you end up in a large room with a curved 'window' out onto space, with covenant with flags up on a ledge. The Minister speaks out about triumphing over the flood. Work your way up along the ridge, slaying the enemy. Cortana says "the security systems in this part of the tower are particularly robust." Keep on going. The Prophet of Truth speaks out again. Checkpoint. Work your way through the rooms. Checkpoint.

"The prophet hierarchs inner sanctum" says Cortana. You go up a slow moving lift. Checkpoint.

Halo 2 Walkthrough

Halo 3 Walkthrough