After the battle with the Brother Moon over Tau Volantis, Isaac Clarke and John Carver wake up on the surface of Tau Volantis, shocked to find out that after falling to their near death, they are still alive, they then make their way across the surface of the frozen planet, finding memories of the horror they had experienced. After finding out that the Marker signal was still causing insanity, suicide and Necromorphs, they battled through more of the threat that Isaac and Carver had just faced. They then found out about a Unitoligist ship that can take them back to Earth. After witnessing many ships lift off, they find out that the Shockpoint Drive in the ship is missing. It can only take them to the CMS Terra Nova.
Once boarding the Terra Nova, Isaac and Carver must find a way to restore power to the derelict CMS Terra Nova and find a new Shockpoint Drive in order to return to Earth. However, within the halls of the old Sovereign Colonies ship, they encounter the remnants of the Circle who've taken refuge inside and begun a new following in the name of the Necromorphs[1]. After dealing with members of the Circle, as well as their own insanity, Isaac and Carver find a new ShockPoint Drive, but Isaac is now losing his mind. He protests installing the ShockPoint Drive into the ship, because he happens to think that if they install the ShockPoint Drive, the Brethren Moons will follow them to Earth, and kill everyone living there. After Isaac and Carver have a hallucination of fighting each other, the hallucination is interrupted by another hallucination, in which the Brethren Moons reveal that they were only slowing Isaac and Carver down, and that they have known where Earth was all along.
After regaining his sanity, Isaac admits that Carver was right all along. He agrees to install the Shockpoint Drive into the Terra Nova. However, Carver then recalls that the Audio Logs hinted that the reactor could power up enough energy in the engine to go into shockspace and return to Earth. They toss the ShockPoint Drive into the reactor, and they overload the reactor by dumping plutonium cores which generates enough power to enter Shockspace. After returning to the bridge, they activate the ship and return to Earth, after attempting to communicate with Earth, they hear transmissions of people getting slaughtered by Necromorphs. When they look out of the cockpit of the Terra Nova, they notice that the Brethren Moons have already arrived and are attacking Earth.
One of the Moons comes up in front of the Terra Nova, crashing the ship and knocking Isaac and Carver unconscious. It is unknown whether this is another hallucination or actually what is happening.