The thunderstorm skull is simple to get. It is a gold skull. It gives all enemies a promotion to the next highest rank.
In order to get this skull, start from the beginning of the level "The Covenant" and fight through the level until you get to the air fight when you are in the Hornet. Fly to the tower that the Arbiter disabled, and land near the entrance. Go ahead and access the terminal that is inside and straight ahead if you feel like it; it's not necessary for retrieving the skull. When you emerge from the terminal area, in front of you should be a ramp extending toward the sea. Walk to the end of the ramp and there you have it, the thunderstorm skull!
Some thing frightening : let’s say an encounter includes 1 Brute chieftain, 1 Brute Captain Ultra, and 5 brute minors. All of them become a rank higher which is very scary (but it racks up a decent amount of points). If you don't mind getting a lot of points by killing 4 captians and fending off 6 minors, then this is the skull for you. This skull is very helpful to get achievments like Guerilla, Demon, Cavalier, Askar, Exterminator, Ranger, Vanguard, Orpheus, and Reclaimer.
EDITOR'S NOTE: Because of the scoring bonus and the fact that flood don't seem to rank up, it's good for "free" points on Floodgate, Cortana and Halo.