While preparing for their next skirmish, the gen:LOCK team receives a transmission from Miguel Garza, who reveals that the Anvil and everyone inside is safe: the late Rufus Weller had figured out Union sympathizers were given a chip that could broadcast a signal to Nanotech so that it would not affect them, and manufactured a copy for the Vanguard that was put into effect when the Behemoth's Nanotech attacked. He then reports that the Union is making another move in Chicago, and needs the gen:LOCK team's help. As the team prepares to leave, Fatima Jha lets Julian Chase know that they are always welcome at RTASA and reassures him that Doctor Weller would be proud. She notices Caliban looking at her, prompting Julian to lead the robot away before he can arouse her suspicions about his true nature.
The team touches down at a pier in the South Side to draw Nemesis to them: after taking out some Union forces they are horrified to realize Nemesis has been upgraded with flight capabilities and Nanotech that can repair any damage. To make matters worse, the Union has modified their Nanotech to respond to a different signal thereby making Weller's discovery useless. The team uses Mindshare to get an edge on Nemesis, but when this does not work they decide to all Mindshare at once. Julian shows reluctance to do so, questioning what this means for him, but before they can try anything they receive a notification that they are almost at Uptime and need to download. Julian chooses to stay in his Holon, exceeding Uptime and leaving him unable to return to his body, in order to buy the rest of the group time.
Nemesis and Julian continue their fight, but when Nemesis realizes how important the team is to Julian he heads to where their real bodies are in front of the Museum of Science and Industry. Before he can attack them, however, he is ambushed by Miranda Worth and Jodie Brennan in their tanks, and Leon August (who had earlier learned he was gen:LOCK compatible but too old for the program) using the Holon intended for Sinclair. Julian realizes without the limits of Uptime he can mod himself freely and continues his fight with Nemesis, buying enough time for the rest of the team to upload back into their Holons.
The entire gen:LOCK team engages in Mindshare, using their combined skills to disable Nemesis's Nanotech and damage him beyond repair. Before Julian destroys him for good, Nemesis hints that the Union made copies of his mind. With the battle over Leon tries to download back into his body, but because of his age the download is not entirely successful, leaving him in a coma that they cannot confirm he will ever recover from.
Colonel Marin congratulates the team on helping them win the battle, and offers them a chance to return to the Anvil. Julian has a talk with Miranda, who sadly remarks that the people they were four years ago died in the Battle of New York, but tells Julian not to be a stranger and that perhaps someday they can try things again. The gen:LOCK team decides to move their base of operations to RTASA, with Migas serving as their chief engineer and liaison to the Vanguard, and Leon moving there to aid in his recovery.
In a post-credit scene, Rob Sinclair, disguised as a Union soldier, moves through a Union-held zone on patrol with others before falling back and hiding in an alley, taking his helmet off to reveal his injured face.
- Julian Chase
- Miranda Worth
- Cameron MacCloud
- Kazu Iida
- Valentina Romanyszyn
- Yasamin Madrani
- Raquel Marin
- Jodie Brennan
- Leon August
- Miguel Garza
- Heng Li Wu
- Fatima Jha
- Rob Sinclair
- The section of Chicago's Museum of Science and Industry that Nemesis and Julian crash through is an exact rendering of the museum's real Earth Sciences exhibit.