On October 27, 2065, the game begins with the Player and their new CO, Jacob Hendricks, infiltrating an NRC Airbase in Ethiopia to rescue Egyptian Prime Minister Said from the NRC with the assistance of John Taylor and his team of cybernetically enhanced soldiers part of the Winslow Accord Black Cyber-Ops Division. Needing to distract the NRC, the Player and Hendricks, along with Winslow Accord Special Forces Team Alpha, use the base's D.E.A.D system to shoot down an NRC plane. Disguised as NRC soldiers, the Player and Hendricks manage to infiltrate the base and rescue Said from the NRC, although they discover there are more prisoners than their Intel provided. The team soon become compromised after Said convinces them to rescue Lt. Khalil, an Egyptian Army veteran and war hero who the NRC plan to use as a tool in their campaign against the Egyptian people. They soon rendezvous with Taylor's Team after being cornered by NRC forces and proceed to escape the base, managing to procure an enemy APC. Before leaving, Hendricks convinces Taylor to rescue the other hostages after reminding that some part of him must still be human. While their escape is successful, the Player and Team Alpha are left behind after their evac harrier sustains heavy fire and bugs out to avoid being shot down, although Hendricks demands that they go back. The Player and Team Alpha are eventually overrun by enemy forces and the members of Team Alpha are killed and the Player is viciously attacked by an NRC Grunt, ripping both the Player's arms off and breaking their right leg until they are found and rescued by Taylor.
Believing that it's the Player's best chance for survival, Taylor brings them to a research installation that specializes in the advanced cybernetic enhancements that Taylor and his team use and decides to use the same cybernetics in order to save the Player's life. The Player is later awakened onboard a train by Taylor, who reveals that the Player had survived the mission but had sustained life threatening injuries in the field. The Player soon learns that the train they're standing in is a simulation created within their DNIs. Revealing that the Player was given one and is currently in a medically induced coma, Taylor explains that their DNI's allows them to communicate with each other on a subconscious level and tells the Player that they have a long way to go. Taylor then introduces them to his unit, which consists of cyber operatives Sebastian Diaz, Sarah Hall, and Peter Maretti during a series of simulations of past battles that were connected with a terrorist attack on a Coalescence train inside the Player's own mind.
Each operative assists the Player in putting the pieces together on how to use their new cybernetics in combat while also helping themselves progress through the simulated terrorist act. Although the Player proves themselves as an efficient soldier, the Player suffers a minor setback when they comes across a group of simulated grunts, causing the simulation to briefly destabilize until they are calmed down by Diaz, who reveals that their DNI can cause certain traumatic memories to seem realistic and can have damaging long term effects if not treated. The Player eventually reaches the final stage of the simulated train bombing and manages to reach the bomb, but is unable to defuse it in time even with their DNI. The Player remains unsure of what to do until they are helped by Taylor, who tells the Player that the solution is actually quite simple. Figuring out that the train car carrying the bomb can be detached from the rest of the train using their DNI, the Player sacrifices themselves by detaching the train car while still inside and the bomb detonates, ending the simulation. Taylor then informs the Player that there was really no way to stop the train despite all the Player's new abilities, telling them that although their DNI can show them all the answers, it'll be be up to them to choose what they have to sacrifice and that sometimes they must let go. The Player is then awoken in the real world and is informed by Taylor that they are being prepped for surgery. Although Hendricks wasn't injured on the mission, he volunteers for the cybernetic surgery as well and both he and the Player are recruited into Taylor's unit.
In 2070, the Player and Hendricks, who are now close friends, are recruited by CIA agent Rachel Kane to investigate the CIA Black Station in Singapore that lost communications. On route they encounter foot soldiers for the ruthless criminal organization the 54 Immortals, who have access to military grade weaponry. Needing to fight through the 54i forces to reach their objective, the operatives are temporarily pinned down by a heavily armoured man of war "Warlord" cyborg before they are rescued by Kane, who then joins Hendricks and the Player in reaching the safe house. Upon arrival, the team discovers the CIA Black Station staff brutally murdered in the ritual "Denial of Reincarnation" and the data drives gone. While they initially believe that 54i enforcer Jae Xiong is responsible for the murders, Kane goes through the entry logs for the safe house and discovers that Taylor's team were the last ones there before arriving. Both Hendricks and the Player are initially unconvinced of Kane's theory about Taylor, having served with him for the past five years.
In order to learn the truth about what happened, the Player and Hendricks then lead an assault on the 54 Immortal's headquarters in the Bio Domes to recover the data drives by posing as arms dealers, making contact with 54i drug dealer Danny Li at a teahouse owned by the 54i. While Hendricks attempts to learn the whereabouts of Jae Xiong, Li states that nobody has seen him in years. After managing to convince Li to work with them, the pair are compromised by 54i leaders and siblings Goh Min And Goh Xiulan, who quickly deduce that the arms dealer are actually members of the Winslow Accord. Greatly out numbered, Hendricks orders Kane to active friendly Grunt reinforcements, killing both Goh Min and Li and forcing Goh Xiulan to flee. After fighting their way to the 54i headquarters, the Player and Hendricks catch Goh Xiulan attempting to decrypt the drives, with Hendricks knocking her out. They then attempt to pull the information out of the drives, but are locked out due to a DNA security system that only allows the Goh siblings to access the console. With Goh Min dead, the Players severs Goh Xiulan's right hand in order to access the console, an act which clearly bothers Hendricks. After obtaining the information from the drives, the pair then escape with Hendricks claiming that what he saw was bullshit, confirming that Taylor and his team have indeed gone rogue.
To understand Taylor's sudden betrayal, the team then use the Intel they retrieved to investigate the site of Taylor's last op, an abandoned Coalescence Corporation facility in Singapore where 300,000 people were killed a long time ago. Within the facility, Hendricks and the Player are both attacked by seemingly inactive Grunts, displaying odd, human like behavior. They discover that the facility was actually a cover for a CIA black project named Project Corvus and later find the decayed corpse's of Jae Xiong and several other test subjects, learning that the CIA were performing DNI experiments on them against their will. They soon learn that Diaz himself is nearby and has hooked himself up to the facility's central CPU core, controlling the Grunts and uploading CIA safe house locations to multiple sources worldwide. Needing to stop the Intel leaks, Kane orders Hendricks and the Player to stop him. While they manage to stop Diaz, the intel was unfortunately sent, revealing every CIA safe house location worldwide. Needing to understand Taylor's motives, Kane orders a reluctant Hendricks to interface with Diaz's DNI, killing the rogue soldier in the process. The team learns that Taylor's squad is currently hunting the two sole survivors of the Project: Dr. Yousef Salim, who is residing in Cairo, and Sebastion Krueger, who's current whereabouts are unknown. They soon become compromised by 54i forces, who were tipped off by the information Diaz sent them before dying. Goh Xiulan, now with a bionic hand, orders her lieutenant to trigger explosives throughout the facility, causing it to flood. While Hendricks and the Player manage to escape the facility, Kane orders them to leave Singapore to avoid being executed by the 54i after her position was compromised by the data leaks.
Knowing that Kane will have no chance of survival if she stays, the Player refuses to abandon her and convinces Hendricks to help rescue Kane from 54i forces, who are currently invading Singapore in vengeful retaliation for Goh Min's death. On route to the safe house Taylor contacts them and claims that he’s told the truth and that the 54i’s wrath upon the citizens of Singapore is righteous. He admits to revealing information to them as well as giving them access to the CIA comm channel protocols. Taylor also mentions that he is doing this to find the Frozen Forest, to which leaves both Hendricks and the Player confused. After reaching the besieged safe house, an explosion knocks back the two operatives, engulfing the building in flames. While Hendricks believes that explosion killed Kane, the Player refuses to give up and attempts to rescue her, but is suddenly attacked by Goh Xiulan in an attempt to avenge her brother, but is ultimately killed by the Player when he/she burns her skull in a bare pipe flare. Walking out of the burning building with a wounded Kane, the Player chastises Hendricks for giving up on Kane. Hendricks mumbles sheepishly "You've got a lot of blood on you."
After escaping Singapore, the team then heads to Egypt to interrogate Dr. Yousef Salim, who had been apprehended by Lt. Khalil's forces. Hendricks, who is on edge, interrogates Salim, telling him that Taylor and his team will kill him unless he reveals what he knows about the project and the Frozen Forest, wanting to know why the rogue unit is obsessed with it. Salim admits that he had worked on the secret project involving illegal DNI experiments on humans, and that his job was to comfort the emotionally unstable test subjects, using the fictional Frozen Forest as a way to keep the subjects calm. Becoming more aggressive, Hendricks violently demands why Taylor and his team are obsessed with the Frozen Forest, but is interrupted by a sudden explosion. Learning that the NRC are attacking, the team assists Khalil and his forces in repelling the attack. Using the assault as a way to distract the team, Taylor and his squad then capture Dr. Salim, although the Player is able to track them using a small tracking chip they had slipped to Salim earlier. Angered over not knowing about the tracker, Hendricks punches the Player hard across the face, accusing them of keeping secrets from him along with Kane. The Player then explains that something is clearly wrong with Hendricks since leaving Singapore, and that they made the call to not tell Hendricks about the tracker. Feeling remorse against striking his friend, Hendricks helps the Player back up, admitting that he shouldn't have taken his feelings about the mission out on the Player, but tells them that everything about it feels wrong.
Elsewhere, Taylor's team interrogates Salim about the location of the Frozen Forest, and then execute him right after Taylor orders Hall to ambush the Egyptian army using a Manticore Mech Suit, needing time to complete his interrogation and escape. While Hall proves to be a challenge against the Player and Hendricks, she is ultimately defeated. Needing to know more behind Taylor's motives, the Player decides to interface with Hall's DNI against her and Hendricks's objections. The Player is surprised to find that Hall's mind is heavily defended in an attempt to find out what she hiding. After fighting through digital defenses of Halls mind and destroying what remains of her subconscious, the Player discovers the presence of an AI virus named Corvus, who had corrupted Taylor and his team during their mission in Singapore, having integrated itself into the DNI's of Taylor's team and slowly taking over their cybernetics, being able to control their actions against their will. After disconnecting with Hall's DNI, the Player tells Kane about the AI and the location of Taylor and Maretti, who have taken refuge on an aquifer controlled by the NRC.
With help from Khalil and the Egyptian army, the Player, Hendricks, and Kane launch an assault on the aquifer in an attempt to capture Taylor and Maretti. During the assault, the Player's cybernetic systems suddenly shut down until they are awakened by Kane, who reveals that Corvus can also infect anyone who interfaces with it, meaning that both Hendricks and the Player are infected as they had interfaced with Diaz and Hall. Continuing the attack, the team decides to lock down the facility in order to trap the rogue soldiers. While they manage to seal Maretti inside, Taylor makes it out and flees on a NRC harrier. During their pursuit of Maretti, the Player and Hendricks continue to experience complication in their cybernetics as Corvus is slowly taking control of them. While the Player manages to fight off Corvus's influence, Hendricks begins to take his frustrations out on the Player, accusing them of losing perspective and even going so far as to threaten to kill Kane, believing that she is somehow behind this until he is struck down by the Player. Telling Hendricks that nobody will be able to help them once Corvus takes control, the Player reminds him of their friendship and that they will need each other more than ever if they are going to fight off Corvus. Managing to bring Hendricks back to his senses, the pair then find and confront Maretti, who attempts to kill them with a sniper rifle but is ultimately killed by the Player when the later kicks him out a window onto a pile of debris, impaling him.
The team then learns that Taylor had made a deal with the NRC in exchange for protection and is currently in Lotus Towers, an NRC stronghold in the city of Cairo. The team then make an attempt to capture Taylor, killing the NRC General Hakim as a way to start a city wide revolution that'll divert the NRC's attention. As they make their way towards Taylor, the Player and Hendricks continue to suffer malfunctions in their cybernetics, experiencing constant system failures and hallucinations as well as hearing Corvus's voice. While the Player is still able to fight of the AI's influence, Hendricks, who had been infected since Singapore, becomes more aggressive and violent towards his own allies, stating that they are fighting a losing battle and that they will make no difference whether they win or lose. After managing to reach Taylor's location, Henricks and the Player attempt to reason with their old leader, who is in a catatonic state. Claiming that he will take them all home, Taylor takes control of the NRC grunts throughout the city, attacking everyone on site including the NRC soldiers. While chasing Taylor, Khalil contacts them and tells them that he is greatly outnumbered by the NRC before his communication cuts out, with Kane confirming that enemy forces captured Khalil. While the Player initially request that they save Khalil, Kane reminds them that Taylor is the priority but promises that they will do what they can once this is over.
After managing to catch up to Taylor, the pair is soon confronted by an army of grunts, with Hendricks staying behind to hold them off while the Player continues to pursue Taylor to the top of Lotus Towers. The Player then fights Taylor, who has commandeered an enemy Mothership. While the Player manages to take down the Mothership, their cybernetic arm is pinned by the ship's debris, partially shutting down other systems, which renders them defenseless. Taylor, who survived the crash unscathed, pulls out a combat knife with the intent of murdering the Player. After desperately trying to convince Taylor that he is not himself, the Player manages to get through to him briefly as Taylor regains his senses and tears out his own DNI through his neck, effectively cutting off Corvus's influence over him. While the Player initially believes that it is over, Taylor reminds them that Corvus still resides in the DNI's of both the Player and Hendricks, making them loose ends. Although the wounded Taylor is no longer considered a threat, he is suddenly killed by Hendricks, who has finally succumbed to the virus and leaves the Player pinned, departing aboard another mothership to the Coalescence facility in Zurich, Switzerland in order to find Krueger.
Kane manages to extract the Player and brings them to the hospital, where the Player tells Kane that they need to stop Hendricks. Kane, not wanting to lose the Player, tries to convince them that they don't have to do this, stating that she can't go on if the Player chooses to go down this path. The Player, set on stopping Hendricks, tells Kane that this is who they are, with Kane leaving behind her bandana and telling the player not to forget her. Some time later, The Player and Kane, who had chosen to remain with the Player out of loyalty, head to Zurich to stop Hendricks. While they have the support of the ZSF, they are hampered on route when Hendricks hijacks the entire city's computer systems and robotic defenders. After fighting through several hacked robots, the Player and Kane manage to breach the Coalescence HQ, discovering that Coalescence has found and replicated the deadly nerve gas Nova 6, having laced the virus into the explosives that killed the 300,000 people in Singapore. Kane attempts to bypass security by initiating emergency protocols, but is tricked and killed by Corvus when it traps her in a room full of Nova 6. Before she dies, Kane warns the Player not to trust in their DNI, knowing that Corvus is nearly complete indoctrinating them. The Player continues on and confronts Hendricks, who is holding Sebastian Krueger hostage in an attempt to know what the Frozen Forest is. The Player makes a final attempt to reason with Hendricks, but is forced to kill him after he executes Krueger in order to prevent Corvus from spreading.
Being the only surviving host of the virus, the Player attempts to commit suicide to prevent them from being controlled by Corvus, but ends up inside a simulated world created within their own DNI. There, the Player is reunited with the digital reincarnations of their teammates, with Hendricks informing the Player that they have reached the Frozen Forest, a place where they can digitally live on after death as their minds have become a part of Corvus's hive mind. Seeing that their former allies have all given into Corvus's influence, the Player continues on until they encounter Corvus with a digital version of Krueger, who also had a DNI, and demands to know why it was created. Krueger argues that every bit of technology embraced by the public presented new ways for their enemies to compromise them, and the DNI was a way of monitoring the thoughts of everybody at once. Corvus was designed to catalogue them. After being told that it was nothing but a mistake, Corvus brutally murders Krueger and destroys what remained of his subconscious. The Player, shocked by what they witnessed, kneels down in despair until they encounter the digitally reincarnated Taylor, who claims that he was the only one to reject the AI's influence before dying which made what remained of his subconscious a virus in Corvus's system. Agreeing to help the Player fight Corvus, Taylor explains that the only way for the Player to defeat Corvus for good is to initiate a system purge in their DNI.
While the Player is still able to fight through Corvus's digital forces, their mental state becomes more and more fractured and they begin to chant Corvus's words, although Taylor's remains their voice of reason and tells them to keep pressing forward. After fighting their way through Corvus's illusory forces, the Player manages to regain control of their body and attempts to purge their DNI. Corvus makes a last ditch effort to control the Player, but is held off by Taylor, who tells the Player to keep fighting. The Player then purges their DNI, causing both Corvus and Taylor to disappear. As the Player stumbles out of the building where the controlled robotics were overrun by the ZSF, a soldier asks the Player to identify themself. As their system slowly completes the purge, the Player says "Taylor" before the screen dramatically fades to black, leaving the Player's non-reality fate unknown.
