Following the events of Assassin's Creed Valhalla: The Last Chapter, the modern-day Assassins use a blood sample provided by Basim Ibn Ishaq to relive his memories during the age of the Abbasid Caliphate. In 861 CE, Basim is a young street thief living in Anbar with his childhood friend and companion, Nehal. For his entire life, Basim has been haunted by visions of a monstrous jinni, which Nehal has been helping him cope with.

While just a simple thief, Basim has greater aspirations and seeks to join the Hidden Ones, but is flatly rejected by the senior Hidden One stationed in Anbar, Roshan. In an effort to prove himself, Basim sneaks into the Caliph's palace to steal a chest sought by both the Hidden Ones and the Order of the Ancients. Basim retrieves a disk-shaped artifact from the chest, which displays a holographic message, before he is confronted by the Caliph, al-Mutawakkil. Nehal kills the Caliph to save Basim, and they both flee the palace. In retaliation for the Caliph's murder, the guards begin slaughtering all thieves in Anbar, including many of Basim's friends, and he angrily blames Nehal before parting ways.

Now on the run, Basim manages to escape the city with Roshan's help, and she takes him to the Hidden Ones' mountain fortress at Alamut. Over the following months, Basim trains under Roshan and is eventually initiated into the Hidden Ones. When their Mentor, Rayhan, learns of the Order's rapidly expanding influence in Baghdad, he decides to send a contingent of Hidden Ones to the city to investigate, with Basim and Roshan leading the way. Upon arriving in Baghdad, Basim learns that five Order members have infiltrated the Caliphate's highest levels of power and are exploiting it to excavate or rebuild ancient Isu artifacts. He proceeds to hunt down four of the Order members, assassinating them and their subordinates and foiling their respective plots.

During this time, Basim reunites with Nehal, who is distrustful of the Hidden Ones and encourages Basim to investigate the artifacts sought by the Order, believing they are both somehow linked to them. Eventually, Basim confronts the Order's leader, al-Mutawakkil's former concubine Qabiha, who claims that the answers he seeks lie in an Isu temple underneath Alamut. Qabiha then tries to convince Basim to accompany her to the temple, but Roshan kills her and warns Basim not to investigate any further. Disobeying Roshan, Basim travels to Alamut with Nehal, only to find the fortress under siege by the Order's forces.

Basim rescues many captured Hidden Ones and rallies them to fight off the attack while he heads to the temple after convincing Rayhan that the knowledge held within could be used to defeat the Order. However, he is confronted by Roshan, who reveals that she is aware of Basim's true nature and attempts to stop him from entering the temple, fearing what it may awaken within Basim. Basim defeats Roshan, but spares her life and enters the temple with Nehal. Inside, he finds more disk-shaped artifacts[c] and discovers that the temple used to be a prison where the Isu Loki was once held.

Basim also realizes that Nehal never existed; both she and the jinni were representations of his repressed memories as Loki. Deciding to embrace his nature as Loki's reincarnation, Basim "fuses" with Nehal and regains Loki's memories. After leaving the temple, Basim is welcomed back into the Hidden Ones, while Roshan resigns in protest. Now fully aware of his past life as Loki, Basim muses that he has been reborn in a new world, and looks forward to a "reunion" with those who were responsible for his imprisonment.

Sometime before his confrontation with Qabiha, Basim is told by his friend Dervis of a painting made by the former's estranged father, Is'haq ibn Khalid, which suggests he is at the ancient city of al-Ula. Having not seen his father since he was mysteriously exiled from Samarra years prior,[d] Basim and Dervis travel to al-Ula together to find answers. During his investigation, Basim learns of a gang of robbers terrorizing the local populace and is captured and imprisoned by their leader, 'Abis.

After escaping and killing 'Abis, Basim discovers that the robbers have kidnapped Is'haq. Following a trail of clues, Basim learns that Is'haq is being held hostage by the true leader of the robbers, a local merchant named Nimlot, who seeks revenge on Basim for killing his father—one of the Order members he assassinated in Baghdad.

Basim infiltrates Nimlot's stronghold and kills him, saving Is'haq, though he is disheartened to learn his father is suffering from dementia and still believes himself to be in Samarra. As Is'haq recalls his past, Basim accompanies him to a nearby tomb, where Is'haq recounts his memories of Basim and Basim's late mother, revealing how much he loves them both.