The game begins in a lunatic asylum on the Sprawl, a densely-populated space station surrounding a shard of Titan, one of Saturn's moons. Currently, the Sprawl is now host to a new Marker, which has led to another Necromorph outbreak. Isaac Clarke has no memory of the past three years, having just been awoken by Franco Delille (protagonist of Dead Space Ignition); however, Franco is killed by an Infector Necromorph and immediately mutates into a monster himself, leaving Isaac to escape on his own. He is later contacted by Daina Le Guin, a woman claiming to have a cure for his "condition". He is also contacted by fellow patient Nolan Stross (a main character from Dead Space: Aftermath), who endured a treatment similar to Isaac's. Daina explains that Hans Tiedemann, the Sprawl's administrator, forced them both to rebuild the Marker after finding Isaac adrift in space near Aegis VII. She further divulges that a self-replicating signal was imprinted on Isaac's mind by his previous encounter with the Marker, putting his life in grave danger, which left Tiedemann no choice but to keep in check by the use of potent memory suppressants. Ignoring Stross, Isaac fights his way through the city (still filled with survivors trying to escape the Necromorphs) to reach Daina. Along the way, Isaac experiences hallucinations of Nicole, which become more vivid as "she" tries to deter him from his task.[20] Upon his arrival, Daina, a Unitologist agent, has Isaac restrained, claiming that they need him to build more Markers to spread Convergence, an event foretold in Unitology, across the universe; before they can leave, however, a Sprawl gunship kills Daina and her associates, allowing Isaac to escape.
Stross contacts Isaac again, claiming that they can destroy the Marker, telling him its location in the Sprawl's Government Sector; left with no choice, Isaac reluctantly decides to trust Stross. As he makes his way there, Isaac comes across Ellie Langford, a CEC pilot who eventually joins their mission. As they travel through the Sprawl, they encounter several obstacles caused by Tiedemann and the Necromorphs. Later, Stross' dementia worsens, causing him to stab Ellie's eye out with a screwdriver; she survives, while Isaac is later forced to kill Stross in self-defense. After further verbal assaults from "Nicole", Isaac comes to accept the guilt of being unable to prevent Nicole's death, causing the visions to become benign.
Upon reaching the Government Sector, Isaac sends a protesting Ellie away alone on a gunship, saying "I couldn't save Nicole, but I can save you, Ellie." Once inside, he sets the Necromorphs onto Tiedemann's forces near the Marker chamber. When Isaac reaches the Marker, he finds it surrounded by Necromorphs, which triggers Convergence. With "Nicole" guiding him, he comes upon the NoonLight Diagnostic Machine (which activates the Marker-affected parts of one's brain, and was used on him and Stross prior to the events of the game) which "Nicole" claims will help him. He then fights his way to the Marker, where he encounters and kills a nearly-defaced Tiedemann. As Isaac approaches the Marker, "Nicole" suddenly pulls him into his own mind, revealing that the only way to make the Marker "whole" is to absorb the body and mind of the one who created it—in this case, Isaac himself. Infuriated and betrayed, Isaac destroys "Nicole" and the Marker codes in his mind in a grueling mental battle, destroying the current Marker in the process.
Waking up, Isaac slumps to the ground, ready to accept his fate. The cumulated damage the Sprawl has sustained causes the station's reactors to enter meltdown. Suddenly, Isaac receives a call from Ellie, who crashes the gunship through the ceiling. As the room collapses, Isaac makes his way onto the gunship, and they escape from the Sprawl as it explodes. On board the gunship, Isaac, sensing a repetition of the previous game's ending, turns to see Ellie, who asks, "What?"
In a post-credits scene, an audio transmission is heard between two people: an unknown subordinate and his ranking superior (known only as "the Overseer" from one of the text logs that can be collected during the course of the game). The subordinate relays that Titan Station (which was Marker Site 12) and the Site 12 Marker have been destroyed. The Overseer replies that the other sites will then have to "pick up the pieces"