The central plot of The Surge 2 takes place in Jericho City, an advanced metropolis surrounded by a giant wall aimed at stemming the advancement of the nanites. It follows an unnamed male or female character, dubbed the "Warrior", who is searching for Athena Guttenberg, the granddaughter of CREO founder Jonah Guttenberg. The Warrior's journey brings them into conflict with the A.I.D. disaster relief unit who are evacuating the city, and the Children of the Spark, a religious cult that worships the Spark, an unstable but powerful source of energy. Led by Matriarch Celeste, the cult believes that the coming of the nanites is foretold by their prophecy of humans ascending beyond mortality by merging with machines. The Children are split into two factions under Celeste's two sons; Eli, prophet and heir to the Spark, and Johnny, his drug-addicted, slovenly brother who uses a physical-enhancing drug to manipulate his underlings. The Warrior is aided by the Stranger, a masked man seeking the truth behind the actions of A.I.D.
Plot
Aboard an airplane, the player character befriends a young girl, Athena Guttenberg. The UTOPIA rocket collides with the plane, releasing its nanite payload which severely damages the craft, causing it to crash on the outskirts of Jericho City. Seemingly the only survivor, the comatose player character is recovered to a prison medical facility. Two months later, the player character is awoken by visions of Athena calling to them as her "Warrior". The prison is attacked by the Delver, a gigantic nanite-creature, freeing the prisoners and allowing the Warrior to escape after installing on themselves a powerful exoskeleton to enhance their abilities. Emerging out into Jericho City, the Warrior learns that the city is now infested with nanites, which are slowly claiming the city and infecting the citizens.
The Warrior meets the Stranger (Warren, the protagonist of The Surge), and they also learn about the Children of the Spark, who believe the crisis foretells the coming of the Spark Incarnate. Brother Eli tasks the Warrior with defeating his brother Little Johnny, so that they can reach the crash site to search for Athena. The Warrior defeats Johnny, but is then betrayed by Eli who intends to claim glory by killing the person who killed his brother. Eli is killed by the warrior. At the crash site, the warrior has one of many visions revealing Athena's journey since the plane crash.
The Warrior pursues Athena's trail to the artificial nature reserve, Gideon Point, where the Delver is hiding. After killing the Delver, the Warrior learns that Athena had taken control of it to release the Warrior from the prison. The Warrior meets with CREO founder Jonah Guttenberg at the CREO Institute of Technology (CIT), and learns that Athena has been captured by A.I.D. Alongside the Stranger, the Warrior infiltrates A.I.D. command and discovers that they have been abducting children under the guise of evacuation and using them in failed nanite-based experiments to try and communicate with the nanite swarm. All of the children have died during the experiments, except Athena because her exposure on the plane changed her, making her more suitable for the experiment. The Warrior defeats General Ezra-Shields who is guarding her, but the process begins before he can interfere. Athena is seemingly destroyed and absorbed into the swarm, reborn as a gigantic nanite serpent. An explosion of nanite activity is triggered, devastating Jericho City.
The Warrior returns to CIT and finds Eli has been resurrected and trying to gain access to Jonah's nanite research. After the Warrior kills Eli for a second time, Jonah reveals that he can remove Athena from the swarm, but that they will require a significant power source, the Spark. Infiltrating the Cathedral of the Spark, the Warrior defeats Eli's mother, Matriarch Celeste, after witnessing her revive Eli again using their own nanite technology. Eli's nanite-infused body grants him superhuman abilities. He leaves with the Spark, believing himself to be the Spark Incarnate that is destined to control the swarm and reshape the world in his own image. Eli kills Jonah and steals his research on connecting with the swarm, which combined with the Spark allows him to steal Athena's powers. The Warrior pursues Eli to the Wall, a massive barrier built around the city, and confronts him.
Eli now possesses near God-like abilities, reshaping himself as Archangel Eli. The Warrior defeats Eli a final time, freeing Athena and her powers, and is given the choice of either executing or sparing Eli. Depending on decisions made throughout the game, Athena takes on her human form composed of nanites and either commends the Warrior for their humanity and compassion, or makes them serve as her guardian because of their lust for power. It is implied that the Warrior died in the plane crash, and Athena used her abilities to revive them as a hybrid of man and nanite. In the aftermath, Athena muses that machines will always be imperfect because they are made by imperfect beings, but that giving them a soul can make a difference.