After you've taken about a third of Set's health, as shown in Phase One, the 3 Marks reappear and you're attacked by a swarm of scarabs, along with various other enemies.
AMMIT also returns, appearing randomly in each of the three corners and attempting to toast you with her fire breath. If you equip fire-resistance items and keep moving, you can effectively ignore her.
NOTE: This is a good time to attempt the Challenge: Catch 5 Enemies in one Blast from a Beacon. See the notes in the main walkthrough for details.
As in phase one, the main objective is to close the Marks and light the beacons. Use remote bombs to deal with the bugs...
...as you close the Marks with the Staff of Osiris....
...and re-light the beacons with your torch. If you take too long to light them, the beacons will go out and the Marks of Set will return, so you'll need to repeat the process.
When all three beacons are burning blue, Osiris once again immobilizes Set. Move to a safe distance and blast Set with the rocket launcher just like you did before.
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