Random Thoughts.....What Are You Thinking?

The story begins with a small crew of miners, among them a man named Sam Caldwell, who are helping to extract the Red Marker from Aegis VII. The crew begins to suffer hallucinations, including Sam, who begins killing his crewmates in what may or may not be self-defense. Before he can escape, a P-Sec squad, including Detective Nathan McNeil, impedes Caldwell's path, and McNeil kills him.

One week later, McNeill, working on the case file of the incidents, meets an old friend, Sgt. Gabriel Weller, now serving on the Ishimura. Upon arrival, the two discover that this outbreak has spread to the entire colony and they are attacked, first by psychotic colonists, then by Necromorphs. They make it to the P-Sec Headquarters, where they discover Lexine Murdoch, Caldwell's girlfriend and agree to take her to safety. The group races to find a shuttle and eventually find one in the Megavents, thanks to a man named Warren Eckhardt, an executive from the mining company. The four of them fly to the Ishimura for help but are warned to return to the surface. The group refuses, resulting in the Ishimura shooting them down, causing the shuttle to crash into the Ishimura and forcing the group to spacewalk to a nearby airlock.

After entering the Ishimura, the group discovers the ship itself is infested with Necromorphs. As they attempt to move to the bridge, which they believe will be safer, they encounter Nicole Brennan in the medical bay who elects to stay behind in case anyone else arrives. The rest of the group continues on but they fall into the sewage system, where Lexine is attacked by Swarmers and pulled into a water tank; the group assumes she has died. Dr. Karen Howell discovers Lexine, who has somehow survived, and the two find McNeill, Eckhardt, and Weller. McNeill, Weller, and Lexine continue on while Howell attempts to shut down the sewerage system, guarded by Eckhardt. While Howell berates Eckhardt for replacing staff with fanatical Unitologists, she is attacked by a Necromorph tentacle. Eckhardt flees and locks the door behind him. When he finds the others, Eckhardt lies, saying Howell locked the door in order to sacrifice her life for the group.

In order to search for a shuttle to get off the Ishimura, McNeill and Lexine split up from Weller and Eckhardt to search multiple shuttle bays. Weller and Eckhardt find a shuttle but Weller catches Eckhardt finishing a recording of a message to a member of the Church of Unitology. Weller watches the message; Eckhardt says that he was sent to find a person who was immune to the effects of the Marker, and who could protect others from its effects as well, and he believes that Lexine is that person. He also explains that he arranged Howell's death because she was beginning to suspect his intentions. When Weller is done watching the message, Eckhardt shoots Weller and tells him of his plans, only to be killed by a Necromorph himself. McNeill and Lexine find Weller and escape on the shuttle right after McNeill shuts down the power to the cannons on the Ishimura that were preventing them from leaving, although he had to cut off his arm in the process. As they escape, they hear a transmission from the USG Kellion. Lexine tries to warn them away but they do not receive the message.
In an epilogue, Lexine is attacked from behind by a Necromorph. The scene gives the impression that McNeill (who had been seeing things and hearing voices, just as all infected do) has transformed into the Necromorph and is attacking Lexine. One can see that the ship she is being attacked on is the shuttlecraft the three protagonists had boarded. At the last moment, she grabs a pistol and aims it at the Necromorph. The scene ends with the muzzle of the gun flashing. Lexine and Weller's story is continued in Dead Space 2's Severed, which again occurs before the game's main events.

An alien artifact, identified as a possible "second Marker", is discovered on the planet Aegis VII. The Church of Unitology uses its influence to send the mining ship USG Ishimura to retrieve this holy relic.

While the ship approaches, they receive radio reports of an outbreak of violent behavior among the colonists. The Marker is brought aboard by order of Captain Mathius (Jim Cummings). Head of Security Alissa Vincent (Nika Futterman) asks to investigate the colony, but Mathius believes that nothing is amiss. While the Ishimura extracts a chunk of the planet to mine, a man in the ship's sickbay struggles against his restraints and resists sedation, begging to be killed.

Meanwhile, two miners on Aegis VII check an outpost that has gone silent. One man vanishes during a blackout, while the other, Colin Barrow, sees his wife Jen (Lia Sargent) commit suicide before his eyes. Barrow takes her body and flees the facility in a shuttle, unaware of an alien presence attaching itself to the corpse.
The Ishimura re-establishes links with the colony, receiving evidence of a bloody massacre and warnings of killers. The Captain refuses to radio for help, as he would face a court martial for entering a restricted system - He instead orders that the planet be quarantined and return to Earth. Before he can be shut out, Barrow's shuttle crashes into the Ishimura's hangar, just as he is killed by his mutated wife. The security team is dispatched to arrest and quarantine the people on the shuttle, but they find nothing aboard the small ship. The man in sickbay awakens to discover alien creatures mutating the corpses in the morgue, which then kill him. Tensions flare as Unitologist crew members demand to see the Marker; they are quickly calmed and dispersed by engineer Samuel Irons (Kevin Michael Richardson), a Unitologist himself.

The security team fight the infestation as it spreads through the ship, with Irons joining them after meeting in the mess hall. Dr. Terrence Kyne (Keith Szarabajka) tells Mathius that the Marker is responsible for the colonists going insane and causing the infestation and must not be taken to Earth, fearing that the Necromorphs will wipe out every last human on Earth if the marker gets to Earth, but the now deranged Captain claims religious persecution and mutiny. Mathius is accidentally killed by Kyne in an attempt to sedate him, who flees the bridge. The ship itself turns against the crew when the escape pods are inexplicably launched empty and their communications systems destroyed, leaving any chance of rescue non-existent.

On the way to the bridge, Vincent's teammate Hanson (Phil Morris) goes insane and kills teammate Shen (Kelly Hu) with a plasma cutter, then is in turn killed by Ramirez (Hal Sparks) with a shot to the head. Vincent, Irons, and Ramirez return to the bridge where they learn that the ship is almost entirely overrun; they then discover that Kyne is sabotaging the ship's engines, to scuttle the ship on the planet below to stop the Necromorphs from spreading.

On their way to confront Kyne, the team finds survivors (Issac Clarke's girlfriend Nicole among them) trapped by Necromorphs. Irons buys time for Vincent and Ramirez to extract the scared crew members by using himself as bait, and is eventually killed. Ramirez then sacrifices himself getting Vincent into the control room - She confronts Kyne, who claims that his actions are necessary to stop the alien outbreak from leaving the system. Vincent fails to restore the engines, and Kyne escapes with her weapon.

Vincent finds herself surrounded by Necromorphs, but learns that the creatures cannot come into close proximity with the artifact, which kept them imprisoned on Aegis VII. Spurred on by a vision of Ramirez's ghost, Vincent leaves a video log that details the entire sequence of events, adding that the Marker and the Ishimura must be destroyed. She uploads the video log to a distress beacon, opens the airlock and launches the beacon from the downed shuttle. Vincent and the Necromorphs are sucked out into space.

Vincent's body drifts in space as the song Twinkle Twinkle Little Star plays. The story ends as the USG Kellion arrives and prepares to dock on the Ishimura - the beginning of Dead Space.

Set in the year 2508, when the USG Ishimura (Japanese: "石村", lit. "Stone Village"), a "planetcracker" starship, sends out a distress signal to the Concordance Extraction Corporation (CEC) during a mining operation on the planet Aegis VII. The CEC dispatches the USG Kellion to investigate. After a guidance system malfunction crashes the Kellion into the Ishimura dock, the crew tries to seek other means of transport. As they explore what appears to be an abandoned ship, they are attacked by grotesque monsters, killing off all but Isaac Clarke, commander Zach Hammond, and computer specialist Kendra Daniels. Hammond notices that many of the ship's systems are failing; he and Kendra direct and assist Isaac in fixing them, so as to keep them all alive for rescue.

As Isaac moves about making the necessary repairs, he discovers various text and audio logs scattered throughout the ship, piecing together the events that transpired prior to their arrival: during the course of its illegal mining of Aegis VII, the Ishimura crew found the Red Marker, the most valuable relic of Unitology, an influential and powerful religion. Captain Mathius, a devout Unitologist, shifted focus, after being asked by the Church of Unitology, from mining to retrieving the Marker. Soon after the Marker's extraction to the Ishimura, humans from the planet's colony and the ship suffered from mass hysteria and violent hallucinations, before subsequently killing each other. Mathius cut off traffic and communications between the two sides, later going insane. Chief Science Officer Terrance Kyne tried to relieve Mathius of duty, only to accidentally kill the captain in a struggle. An alien virus, the genetic coding of which is encrypted on the Marker, then began ravaging the Aegis VII colony, infecting any available corpses and turning them into "Necromorphs" - mutated and reanimated corpses that violently slaughter infected humans to spread the infestation. A colony shuttle carrying an infectious Necromorph caused the scourge to spread across the Ishimura. Though Hammond states that he is unaware of what the Marker is, Kendra confides to Isaac that Hammond may be lying. Isaac later encounters his girlfriend Nicole Brennan, a medical officer aboard the Ishimura, though they are unable to meet.

After repairing the critical systems, Isaac's team launches a second beacon, attracting the nearby USM Valor; however, the Valor, having picked up an escape pod with a Necromorph inside (launched earlier by Hammond) is overrun and crashes into the ship. Hammond deduces, from the military equipment he finds on board, that the Valor was actually assigned to destroy the Ishimura. Deciding that they must escape while they can, Isaac and Hammond retrieve the Valor's power core in order to repair an available shuttle, though Hammond is killed by an enhanced Necromorph in the process. Dr. Kyne, one of the last survivors of the Ishimura, later contacts Isaac, urging him to return the Marker to Aegis VII, believing that it can restrain the "Hive Mind", a creature that controls the Necromorphs (though originally created for military purposes). After assisting Isaac in loading the Marker onto the shuttle, Kendra murders Kyne, revealing herself as a government operative ordered to retrieve the Marker for her superiors. She reveals that the Marker is a reverse-engineered copy of the Black Marker found on Earth, placed on Aegis VII by the government to monitor its effects. She then leaves on the shuttle without Isaac, but Nicole arrives and is able to help him recall the shuttle via remote pilot, prompting Kendra to flee via escape pod.

Isaac takes the Marker back to the colony, pacifying the Hive Mind and creating a "dead space" that makes all Necromorphs in the surrounding area dormant (it is revealed in the "backstory logs" unlocked by completing the game that "dead space" refers to the area surrounding the Marker wherein the infection and reanimation processes are subdued by the emission of various types of signals from the Marker). However, this also disrupts the gravity tethers keeping Aegis VII from tearing itself apart. As Isaac attempts to escape the planet, Kendra appears and starts to take the Marker back to the shuttle. She shows Isaac, through a recovered distress transmission, that Nicole committed suicide via lethal injection before Isaac's team arrived on the Ishimura; his visions of her were the Marker's attempts to bring itself back to the planet. Isaac intercepts Kendra loading the Marker back into the shuttle; before she can leave, however, the Hive Mind reawakens, violently killing her, leaving Isaac to defeat it in a ferocious battle.

Leaving the Marker behind, Isaac flies off in the shuttle before the colony is destroyed. As he sets course away from Aegis VII, Isaac removes his helmet and watches Nicole's first transmission again; now knowing how it ends, he turns it off before it can finish. Noticing something in his peripherals, Isaac looks to his right and is attacked by a vision of a bloody Nicole, just before the scene cuts to black.

In Dead Space, the player takes on the role of a figure known as Vandal, a newly converted Unitologist, on a mission in the mines of Titan Station, orbiting Saturn. Vandal is directed over his headset to destroy a series of power boxes, thus cutting off communication to certain parts of the station. After doing so, however, he is attacked by a group of Necromorphs, and is forced to flee towards a tram system. On his way there, the head of Unitology, Daina Le Guin, tells Vandal that he has released a Necromorph infestation onto the station and that his death, and the deaths of all the miners, will be a glorious event. Vandal tells Le Guin that he is determined to inform the government of what the church has done. Meanwhile, the director of the station, Tiedemann, gets in touch and orders Vandal to restore the quarantine seals. After doing so, Vandal is contacted by Tyler Radikov, his Unitologist contact, who swears to him that Le Guin duped him too, and he had no idea what Vandal's real mission was. Radikov promises to guide Vandal in his escape.

Under the direction of Tiedemann and Radikov, Vandal heads to lockdown the doors to the Public Sector of the station. Radikov tells him that in order to do so he must shut off the power to the seals, as this will trigger all emergency seals to engage and will protect the Public Sector. Vandal does so, but discovers that Radikov has been lying to him, and he has in fact opened the doors of the Public Sector to the infestation. A furious Tiedemann then demands that he try to shut down the core of the station, as it is overheating, and is in danger of destroying the entire station.

When he reaches the core, he sees a large Necromorph "suffocating" it. He defeats the creature, but falls into the core with it. After several moments, Vandal manages to crawl out of the core, where it is revealed to the player that he is actually a female, and tries to radio for help, leaving an audio log telling whoever finds it of what has happened. The game ends with Radikov telling Le Guin that the Necromorph outbreak was a success. Back at the core, Vandal is gone, with a trail of blood leading off-screen, and only her helmet remaining.

Set between the events of Dead Space and Dead Space: Aftermath, a group of freelance miners, known as "magpies," discover the abandoned USG Ishimura in deep space. Their once-fortunate luck turns into a catastrophe as they realize they are in the middle of a living nightmare. Not only is the Earth Government racing to claim the Ishimura, but the Necromorphs are also reanimating across the ship.
Captain Benedykt Malyech of the Magpie ship Black Beak is chased in the halls of the Ishimura by a multitude of Necromorphs and subsequently turns into one before waking up. His adjutant, Julia Copland, comforts him before directing their attention to a motherlode of minerals.

In the meantime, the Earth Government's Defense Secretary David Chang arrives at the Aegis VII blockade. He is on orders to find the Marker and the Ishimura, both of which they are unable to locate. In addition, they are joined by the Oracles, who take control of the situation.

We return to the perspective of the Magpies, who are using a shockring to transport eggs (clumps of minerals) to their Nest (a large storage ship) when they get an odd reading. The Ishimura is shocked into their position and destroys their Nest with its captain, Bellevin, and damages the Hunter Moon, a ship commanded by Jessica Li and Stefan Schneider. They manage to use gravity tethers to hold the Ishimura in position and begin boarding.

The Ishimura is heavily damaged with most systems nonfunctional or malfunctioning. It is devoid of people or Necromorphs but is instead full of an organic sludge. Gatura Okeke, Stefan and Jessica explore the ship while Malyech investigates crystals on the side of the ship, which turn out to be Marker fragments; but when he gets too close to them, he blacks out and has a nightmare of being chased by an Ubermorph-like Necromorph. When he wakes up, he takes the shards and goes to the Ishimura.

Jessica decides to salvage the ship for parts and gathers the crew at the bridge. While they discuss the fate of the crew, Malyech shows them the pieces of the Marker. Li proposes selling the Marker shards, which prompts Malyech to assault her. He is brought down after a brief struggle and Venschiff, one of his crewmates, locks him up in the brig.
The crew realize that there might be a whole Marker on board but are panicked when Copland leaves for the EarthGov blockade with a few Marker shards. Li rallies the crew and gives them all tasks. Okeke goes down to engineering to repair the shockpoint drive. She also goes to see if Malyech has regained sanity. The rest of the crew keeps a lookout for EarthGov. Julia arrives at the EarthGov blockade and is not taken seriously until she produces Marker shards. Chang agrees to negotiate with her for a deal, but the negotiators are the Oracles. After revealing all the information, she asks for a "reward or something". Copland receives "something": death.

Malyech is awakened by a hallucination of Bellevin in the brig. It occupies his attention by informing him that he needs to be made whole. Meanwhile, the Necromorph biomass reanimates and consumes him, making him whole. Around the same time, Venschiff loses his mind and attacks Stefan in a paranoid frenzy. He tries to strangle Stefan but in retaliation, Stefan stabs Venschiff with a Marker fragment.

After the remaining logs are scanned, the crew realizes the Marker isn't on board. They relay the news to Li who is being stalked by a Necromorph. Just as they hear its hissing over the com, Malyech's Necromorph form drops down and kills Li. Suspicious, the crew decides to head down to Li's level, where a large Brute-like Necromorph rips Thorssen and Gottheddir to pieces in rapid succession. Stefan and Wenbo open fire on it but when Stefan destroys a relay, both the Brute and Wenbo are blown to bits. Stefan survives and warns Okeke to leave, but he and his crew are killed by more gargantuan Necromorphs in the engine room.

Both the Oracles and EarthGov arrive on the Ishimura, but the Oracles come on a stealth shuttle. Stefan speaks with the Marines and tricks them into going to the Cargo Bay, which contains Necromorphs. The Oracles realize the trick but leave them to their fate to buy time. They then proceed to activate quarantine protocols. The Marines led by Captain Amise search the Cargo Bay for the Marker and Stefan, but instead find Necromorphs and death.

Stefan fights through the Necromorphs but is trapped by the quarantine. While Stefan figures a way out, the rest of the EarthGov team is killed. Meanwhile, the Oracles destroy Necromorphs with ease using strange weapons. When they reach the Bridge, they realize that the Marker is destroyed and that Stefan was doing a space walk. They follow and confront him but are interrupted by a Hive Mind. The Oracles dispatch it and they continue their confrontation with Stefan inside. They corner Stefan but he threatens to shocking them all with a remote control. The Oracles partially reveal their motives but stop when they realize the 'remote control' is really just a radiation detector. Stefan makes a break for it and escapes through a hatch. The Oracle with the weapon loses his arm when the hatch shuts. Both the Oracles are then eviscerated by a mob of Necromorphs.

Stefan uses their strange weapon to fight his way through the Necromorphs. His ship is swarmed by them so he decides to use the stealth shuttle of the Oracles in order to escape. He contacts EarthGov and informs them of the Ishimura's location. Chang orders him to stay, but Stefan insults him and shocks out to an unknown destination.

When contact with the USG Ishimura and the Aegis VII colony is lost, the Concordance Extraction Corporation sends the ship USG O'Bannon to investigate. But the corporation loses contact with the O'Bannon as well.

The Marine battleship Abraxis portals to and docks with the O'Bannon. Five marines board the ship and see mutilated bodies. Their scanners detect four people still alive: Nicholas Kuttner, a security officer; Alejandro Borgas, an engineer; Nolan Stross, chief science officer; and Isabella Cho, chief medical officer. Kuttner starts shooting at the marines, wounding a marine. The marines incapacitate them and take them to the Abraxis. The Abraxis then destroys the O'Bannon and portals out of the Aegis system. The four find themselves in a holding cell on the Abraxis, heading to the Sprawl, a station built on a shard of Titan. The head interrogator is told by the Overseer he has seven hours to get information from the survivors.

Kuttner is interrogated first. They use his fear of being burned alive to get him to cooperate. Kuttner's daughter, Vivian, was killed prior to the mission. He was in a conference room with Cho, Stross, a soldier named Rin and their leader Sergenko. Borgas enters the room with his 19-year-old cousin Noah and Omar, a Unitologist. All three were picked up from the Sprawl. Captain Campbell enters and explains that crews will stabilize the gravity on Aegis VII, then dismisses the engineers. Campbell explains that Kuttner's crew are to bring back pieces of the Marker, which are worth millions of credits per kilo. The crew and engineers land on Aegis VII, which has become dangerously unstable. While the engineers work the gravity stabilizer, Kuttner's crew split up. Kuttner finds a shard of the Marker which has a terrible effect on him. He sees a vision of his daughter. His hallucination of the crew as monsters trying to hurt her causes him to attack the engineers. He kills Noah and causes the stabilizer to malfunction, and his teammates tie him up in the shuttle.

After giving his account, the restraints are removed. Kuttner kills several crew members before he is shot. He sees his daughter walk through an airlock. As the marines attempt to grab him, he opens the airlock, killing himself and the marines.

They bring in Borgas, who explains the crew made it to the shuttle, but Rin, Sergenko and Omar were killed. Borgas was forced to crash land the shuttle onto the O'Bannon. Aegis VII explodes seconds before the ship can jump out of the system. The debris causes severe damage to the ShockPoint Drive. Borgas, enraged by his cousin's death, demands to know the importance of the shard. When the captain explains the shard's monetary value, Borgas assaults him. After Cho calms him down, he follows the captain's order to fix the drive.

After giving his account, the lead interrogator assures Borgas he will go home. He has Borgas killed. He sends in Stross. Stross' account begins after getting the shard on the ship. Stross was on the O'Bannon with his wife and infant son, but his duties were taking a toll on their relationship. He studies the shard, which begins to affect him. He sees symbols everywhere and begins to obsess over the Marker. He explains to the captain how the Marker was possibly designed by a higher power; and how it takes dead flesh and restructures the DNA, improving it. To prove this theory, he takes a body from the morgue and exposes it to the shard. The corpse transforms into a Necromorph and begins killing and transforming crew members throughout the ship. Stross runs to his living quarters and kills his wife and son, thinking they are Necromorphs. The head interrogator, realizing that Stross can communicate with the Marker, has him stored.

When Cho gives her account, it is discovered that she was having an affair with Stross, and she had fallen in love with him. She noticed changes in him after he began to study the shard. After having sex with him in the lab, they have an argument and he tells her to leave. After checking up on Kuttner, she and several other doctors arrive at the morgue. They find the bodies gone and several doctors killed. One of the bodies turns into a Necromorph, causing the group to flee. She releases Kuttner, who kills the Necromorph. She goes to Stross' living quarters, and finds he murdered his wife and son. They eventually meet up with Captain Campbell, who is fighting the Necromorphs with the security team. The Necromorphs overwhelm the last of the security, and the Captain, Kuttner, Cho and Stross flee into the vents. They make it to Stross' lab, where they meet with Borgas, and two officers from the bridge. Stross explains that destroying the shard could stop the Necromorphs. Borgas says that throwing it into the portal drive could not only destroy it, but restart the drive. With weapons made by Borgas, they head to engineering. Debris from the planet causes a hull breach, damaging the outer door control for engineering. Captain Campbell sacrifices himself to seal the door manually. The four survivors battle the Necromorphs to get to the portal drive. When Stross refuses to throw the shard into the drive, Cho does it. The drive's energy destroys the shard, which causes all the Necromorphs to liquefy.

After giving her account, Cho is informed that the Abraxis has reached the Sprawl. Cho surmises that her superiors are aware of the effects of the Marker and are using those exposed as human guinea pigs. The Overseer accompanies Cho to the Sprawl and has the interrogator and his assistant killed. The Overseer offers Cho a position as head of the project, but Cho refuses after seeing what her superiors have done. She is lobotomised.

The Overseer and his assistant watch a news report where a lobotomised Cho is accused of being a terrorist responsible for the Ishimura, Aegis VII colony, and O'Bannon disasters. They then discuss studying Stross, highlighting their luck in finding two people who have come into contact with the Marker. They proceed to store him in the lab where, in the slot next to him, is the other person - the crazed engineer that they found floating in a shuttle weeks ago who was responsible for destroying Aegis VII. The name of the engineer, Isaac Clarke, is then seen on a holographic monitor, marking the beginning of Dead Space 2.

Plot:
The official EA press release outlined the basic plot of Dead Space Ignition, revealing that the game "takes place on the Sprawl [the setting of Dead Space 2] and challenges players to survive the initial Necromorph outbreak", which then sets up the plot of Dead Space 2. Executive producer Steve Papoutsis suggested that the game, the first of a number of related additions to the series, "will give Dead Space fans a unique perspective on the events leading up to Dead Space 2, and will also introduce the storyline to a brand-new audience of gamers."

Story:
Dead Space Ignition takes place before the events of Dead Space 2. An engineer named Franco Delile (the player character) and his partner Sarah are called to fix an elevator on the Sprawl, only to discover evidence of sabotage. They are then called to fix a computer mainframe, again finding that the damage was intentional. While traveling between jobs, they hear distant screams and investigate, only to encounter people being attacked by grotesque monstrosities dubbed "Necromorphs." Franco and Sarah escape using the tram. From there on, they are sent across the Sprawl in an increasingly desperate attempt to repair station systems and assist other survivors, all the while under attack by Necromorphs. Depending on the player's choices, Sarah may be killed by asphyxiation, Necromorphs, or by Franco after receiving a coded message. The story ends with Franco reaching the Sprawl hospital, and reviving Isaac Clarke, leading up to the opening scene of Dead Space 2.

The game begins in an asylum on the Sprawl, a densely-populated space station surrounding a shard of Titan, one of Saturn's moons. Isaac Clarke has no memory of the past three years, having just been awoken by Franco Delille (protagonist of Dead Space Ignition), who is attempting to free him. Unfortunately, a Necromorph outbreak claims Franco's life, 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 Sprawl administrator Hans Tiedemann is building a new Marker using information encoded in both Clarke's and Stross's brains. She also claims 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. 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; however, an EarthGov gunship strikes, killing Daina and her associates and 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. (This is where I'm at in the story) As they travel through the Sprawl, they encounter several obstacles caused by Tiedemann and the Necromorphs, eventually forcing Isaac to venture back inside the Ishimura, which is docked at the Sprawl for decontamination and repair after to the events of the first game. Additionally, Stross' dementia worsens, causing him to stab Ellie's eye out with a screwdriver; she survives, but Isaac is forced to kill him in self-defense. And, after weathering further verbal assaults from Nicole, Isaac comes to accept the guilt of being unable to prevent her 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 and uses 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. He then fights his way to the Marker, where he encounters and kills Tiedemann. At this point, the Nicole hallucinations pull Isaac 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.

Waking up, Isaac discovers that the Marker has been rendered nonfunctional, and that the accumulate damage to the Sprawl have resulted in its reactors melting down. Isaac slumps to the ground, ready to accept his fate, and the credits roll... only to be interrupted by Ellie, who crashes the gunship through the ceiling. The two escape as the Sprawl explodes.

In a post-credits scene, an audio transmission is heard between two people: an unknown man 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 he calls "Marker Site 12," and its Marker have been destroyed. The Overseer replies that the other sites will then have to "pick up the pieces".

Two months after escaping the Sprawl, Isaac Clarke and Ellie Langford encounter Sgt. John Carver, a survivor of a Necromorph incident on the planet Uxor; and discover Tau Volantis, a frozen planet where the ruins of another planetcracker ship are found. Realizing that these miners had found the "source" of the Markers, the group tries to land on the frigid planet; however, the ship breaks apart upon entry, and Ellie is separated from the others. As a result, Isaac resolves to save her along with his original goal of stopping the Markers. Many of the obstacles the two must face include a new human enemy, Unitologist soldiers; environmental hazards like falling machinery and a giant mining drill; and new variants of Necromorph, like the giant insect-esque Nexus and the more deceptive Wasters.