After returning from Washington DC, Andromeda tells Ford that she has figured Adams path, he seems to be traveling from one progenitor signal to another, and when he does, the signal disappears. Ford knows that this means that Prometheus' speculation about Adams killing the progenitors is correct so he ask Andromeda to send him to the next signal in his path. However, the ship's Conduit Dialer has lost power doue to being abandoned for so many years, so Andromeda sends Ford to reactivate power core of the ship. Ford then goes to explore the remaining of the ship. Andromeda also introduces Ford to the Arsenal Replicator, explaining to him that he can bring any weapon or upgrade blueprint and get an exact duplicate for him to use at any time he visits the hub.Shortly, Ford reaches the first area he visited on the ship, however the Leviathan that brougth him is no longer there. A new platform appears, leading Ford to a new door on the upper level. After crossing the door, he finds a new enemy, the imposing Guardian sub-boss enemy.
After bringing it offline, Ford is free to continue exploring the ship, but will discover that many sections are flooded, and due to the lack of maintenance, the water will be electrified. Shortly after, he will encounter two more Guradians, but he manages to deactivate them. During a short tunnel section free of powerful enemies, Prometheus reveals to Ford that he fought alongside Andromeda centuries ago, and that she was an exceptional warrior, but she believes he betrayed her. Andromeda interrupts the conversation to ask to Ford if he got to the power core, but he complains that he is not getting any help.
Ford finally gets to the power core, but two more Guardians awaits him, to make the mission easier, he tan take them out from the entry point, so he can at least stay away from their melee attacks. After dispatching them, he proceeds to get to the main console. With the ASE, Ford hacks into the system, restoring the power to the main conduit and also unlocking a door that leads to the beginning of the central area of Atlantis. After getting back to Andromeda, she discovers that Ford has been in contact with Prometheus, and tells him that Prometheus has not told everything to him, explaining Ford the origins of the ASE, something that Prometheus never explained to him before. Still, Prometheus tells Ford that he has to trust him on this one.
With the Conduit Dialer now working, he can select any destination he had previously discovered on the levels. If he found everything in the previous missions, he will have six destinations to choose, with China and Crash Site being the new ones.