In 2020, the unexplained strengthening of Earth's magnetic field negatively affects the planet. Layla Hassan, Shaun Hastings, and Rebecca Crane receive a signal with coordinates in New England, where they exhume a Viking raider's remains. Layla, struggling with the Staff of Hermes Trismegistus' influence, enters the Animus to view the raider's memories.

In 855 AD in Norway, a young Eivor Varinsdottir witnesses warlord Kjotve the Cruel sacking her hometown and killing her parents before she is rescued by Sigurd, son of King Styrbjorn of the Raven Clan. Seventeen years later, Eivor has been adopted by Styrbjorn, and pursues vengeance against Kjotve. Her latest attempt fails, but she recovers her father's axe.

Touching it, Eivor experiences a vision of Odin, leading her to consult the local seeress, Valka. Valka induces another vision of Sigurd losing an arm before being consumed by a giant wolf. Sigurd returns from an expedition with foreigners Basim Ibn Ishaq and Hytham, members of the Hidden Ones, who came to Norway to eliminate Kjotve, a member of the opposing Order of the Ancients. Defying Styrbjorn's orders, Eivor and Sigurd enlist King Harald's help to kill Kjotve. Following their victory, Harald declares his intention to unite Norway under his rule. Styrbjorn pledges fealty to Harald, angering Sigurd, who expected to inherit the crown.

He and Eivor take loyalists in the clan on an exodus to England, where they establish their own settlement named Ravensthorpe. After setting up Ravensthorpe, Eivor focuses on securing alliances with neighboring Saxon kingdoms and Viking clans. She aids the jarlskona Soma in reclaiming the town of Grantebridge from the Order of the Ancients; befriends the Sons of Ragnar led by Ivar, Halfdan, and Ubba Ragnarsson; helps install Ceolwulf and Oswald as Kings of Mercia and East Anglia, respectively; and settles a conflict with King Rhodri of Wales, during which she is forced to kill an increasingly bloodthirsty Ivar.

At Hytham's request, Eivor also tracks down and eliminates Order members operating in Lunden, Jorvik, and Wincestre, following tip-offs from a "Poor Fellow-Soldier of Christ." Eivor's hunt for one Order member takes her to Vinland, where she recovers a strange artifact and gives it to the native Kanien'kehá:ka.[g] Eivor's visions continue. Valka gives her an elixir that makes her dream of Asgard from Odin's perspective. Hoping to avert his own fated death during Ragnarök, Odin imprisons Loki's son Fenrir, who is foretold to kill him, and retrieves a magical mead from Jotunheim that will allow him and the other Aesir to be reincarnated.

Layla realizes these are actually visions of the Isu shortly before the Great Catastrophe, and that Loki, who was forbidden to reincarnate himself after betraying Odin, found another way to ensure his survival. Sigurd and Basim discover an Isu relic, and Sigurd, with Basim's encouragement, comes to believe himself a god. Fulke, an Order agent and servant of King Alfred of Wessex, captures Sigurd, believing him to be an Isu or descendant thereof, and tortures him, removing his right arm.

Eivor rallies her allies to kill Fulke and rescue Sigurd, who has also begun experiencing strange visions. Eivor later accompanies Sigurd back to Norway to investigate his visions, finding an Isu temple with a tree-shaped computer system. The siblings connect themselves to it and are seemingly transported to Valhalla, where they enjoy endless battles, until Eivor realizes it is just a simulation. Having become disillusioned with the pursuit of glory, Eivor persuades Sigurd to return to the real world, and escapes the simulation after resisting Odin.

Upon awakening, Eivor is confronted by Basim, who reveals himself, Eivor, and Sigurd to be reincarnations of Loki, Odin, and Tyr, respectively. Seeking revenge on Odin for Fenrir's imprisonment, Basim attacks Eivor, but is defeated and trapped in the simulation. Sigurd then abdicates leadership of the clan to Eivor, who returns to England. Later, Eivor and her allies join Guthrum's assault on Wessex, defeating Alfred's forces at the Battle of Chippenham. Eivor tracks down Alfred, who reveals himself as both the leader of the Order and the "Poor Fellow-Soldier of Christ."

Disgusted by the Order's heresy against Christianity, Alfred sought to replace it with a new God-fearing order. Eivor spares Alfred and returns to Ravensthorpe to a hero's welcome. In the present, the Assassins deduce the strengthening magnetic field is a result of Desmond Miles' activation of the Isu towers in 2012. To stabilize the field, Layla travels to the Norway temple and enters the simulation. She meets Basim, who reveals that he led the Assassins to Eivor, and tells her how to stabilize the magnetic field.

She does so, but this releases Basim and traps Layla in the simulation. Layla encounters a being called "the Reader," and decides to work with him to prevent future disasters, allowing her mortal body to die.