Atlatea is the name of the city ship that the Masari used to reach Earth. When they went into stasis, they sank the ship under the water which explains the legend of Atlantis. Queen Altea also relies on this ship to supply her power.
During the Hierarchy campaign, the Hierarchy accidentally tripped an alarm in the ancient pyramids that seemingly forced them to retreat, even against the orders of Kamal Rex and Orlok the Eternal (the units claimed it was a "hard-wired" retreat). The ship sent out signals that disrupted the Purifier's production. A Hierarchy force led by Orlok came to the ocean where they found the source of the signal was from the Masari ship. It then rose to the surface and Kamal refused to accept that the "Gods" still existed.
He (Kamal) then ordered an orbital bombardment from the Hierarchy orbital fleet. The ship is severely damaged but not altogether destroyed, and the Hierarchy invaded the ship to prevent repairs and the cryo stasis pods containing the Masari to open while facing increasing resistance from Masari Disciples. Overall, they were unable to prevent the Masari from awakening and as such they were free to fight their enemies.
In a Global Conquest game, Atlatea serves as the Masari's main base structure. Like other base structures, if it's ever destroyed, the player controlling it loses.