A few years after Helix Security International was hired to defend the Giza Plateau, the Anubis A.I, a God Program, broke free. An engineering team was sent to contain it, but nothing had been heard from them. Helix sent in a team to help, composed of Captain Khalil, Lieutenant Pharah, Tariq, Saleh, Mahmud, Okoro (an omnic), and Aizad, among others.
The team finds one of the engineers badly injured. He tells them that the sentry bots had recognized them as a threat to Anubis and opened fire. Tariq points out that if Anubis breaks through Helix's firewalls, it could spread to other parts of the globe, corrupt infrastructure, and launch military assaults. Though Mahmud and Saleh want to give the engineer medical support, Pharah insists on moving along as they don't have much time. Khalil takes her aside to point out that if she wants to be a good leader, she needs to focus on her team's well-being and treat them like a family.
Okoro interrupts their conversation to announce that Anubis' omnics have set up an ambush, and that they are taking control of him as he speaks. He shoots himself in the head to prevent himself from turning on his team. Infected omnics appear and begin firing from shops, alleyways, and rooftops, starting a battle in which many Helix guards are struck down and Khalil is killed. Pharah, Saleh, and Tariq are the only ones remaining. Pharah decides to take Khalil's words to heart and encourages the troops to take on Anubis directly.
The three enter the Temple of Anubis to a horde of infected omnics that immediately begin firing. Saleh is struck down as Tariq and Pharah take out many sentries. When Pharah finally gets a clear shot at Anubis itself, a pillar is knocked over and begins to fall on Tariq. Pharah makes a split second decision to push him out of the way, losing her last missile in the process. At first, Tariq is confused by Pharah focusing on him rather than the mission, but shrugs it off and comes up with an alternative method to disable Anubis: while Pharah buys him some time, he could create a feedback loop to paralyze the omnics. The plan is successful, and Pharah, Tariq, and Saleh leave the temple.
As Saleh is taken into a medical bay, Pharah tells him that Khalil was killed in the fight. Saleh says that she would be captain now, and that he will gladly fight with her.