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The portal-storm was first seen in the Halo 3 Announcement Trailer. When the camera shows the artifact being uncovered and activated, the storm lies directly over it. Lightning bolts are seen flashing out of the clouds. The formation seems to have an eye, like a hurricane would. When the portal is activated, the beam travels up through this eye and disappears.
In Halo 3, in the level Crow's Nest, when a player looks up at some of the computer monitors, a map of the local area can be seen. The map will have a mass of clouds beginning to show a swirling motion around the area. In the level Tsavo Highway, a doughnut-shaped mass of clouds can be seen above the artifact that the Covenant are digging up.
If one looks to their left in the hangar in Crow's Nest, past the cruiser, you can see the artificial storm.
When proceeding the level the Storm, which is presumably named after the storm above the portal, the storm has intensified and grown. The clouds now bring rain to the area, and certain parts of the cloud glow as if cloud-to-cloud lightning is occurring. At a point in the level, a group of UNSC Marines are present around a radio. Intel comes over the communications channel and says "...winds inside the storm have been clocked at over 200 kilometers per hour." When the Prophet of Truth activates the Portal, the solid blue beam shoots up into the cloud formation's eye and opens the portal to the Ark.
After the portal is opened, and the level Floodgate begins, the remains of the clouds are seen broken up and swirling around the portal in the sky, having been disrupted by the opening of the portal itself.