If the cutscene at the Scarab doesn't trigger, check if a Brute fell off the ledge and survived. All the Brutes must be dead.
Kill the Elite who brings forth the Spectre, drive ahead and park it behind the rock, and hijack a Ghost. Deloading door enemies: At the door guarded by 2 Wraiths and several Brutes, it's possible to trick the game into thinking the battle's been won. Generally, you'd drive up to the door, get to cover, face away from the enemies, and start shooting for about 15-30 seconds. If you did it correctly, most if not all of the enemies should be gone.
Swag jump: It's possible to drive the Ghost across the gap. Needs more info
Prison: Release the Hunters, kill enough enemies to open the door and drive past the reinforcements.
Deloading Wraith pilots: Immediately after the cutscene ends, go back to the previous room. If done correctly, the 3 Wraiths should have their drivers removed from the game, allowing the Scarab to proceed.
Spectre strats/Cloning Johnson: Drive the Spectre to the spot which allows you to enter the control room early. Wait for Scarab to blow up the door, then park the Spectre near the edge, facing the structure, and get out. Time it so you trigger the cutscene as the Spectre is about to fall off. If done correctly, it should be waiting for you in the backroom. Use this to clone Johnson by making him get in. Make sure to kill non-gold Elites so they don't get in it. Johnson should respawn at the same time as Miranda. When you have 2-3 Johnsons in your Spectre, just drive down to Tartarus, stick it with a plasma, and enjoy the carnage.