Odyssey's story begins in 480 BC, where King Leonidas leads the Spartan army against a Persian charge during the Battle of Thermopylae. The skirmish is won, but Leonidas is informed by a captured enemy that the Persian army has learned of the mountain path and will surround the Spartans by morning. Nevertheless, Leonidas resolves to hold off the Persian advance. In 2018, Layla Hassan recovers Leonidas' spear and extracts from it the DNA of his grandchildren, Alexios and Kassandra, to be used for her Animus to find the location of the Staff of Hermes Trismegistus. Whichever sibling is selected by the player (and therefore, by Layla) is designated as the Eagle Bearer.
On the island of Kephallonia, The Eagle Bearer is recruited by a mysterious merchant named Elpenor to assassinate the "Wolf of Sparta" in the polis of Megaris, and departs Kephallonia after befriending a naval captain named Barnabas and assuming command of his ship, the Adrestia. During their time in Megaris, the Eagle Bearer learns that the "Wolf of Sparta" is in fact the sobriquet of Nikolaos; that Nikolaos is not in fact their biological father and has another adopted son, Stentor; and that their mother Myrinne left Nikolaos and Sparta shortly after the incident at Mount Taygetos. The Eagle Bearer travels to Phokis to confront Elpenor, who reveals himself to be a member of the Cult of Kosmos and is aware of their lineage as the grandchild of King Leonidas. Disguised with Elpenor's mask and robes after killing him, the Eagle Bearer infiltrates a secret Cult meeting in Delphi where they discover that their younger sibling had survived the fall from Mount Taygetos, but is corrupted and twisted as part of a plot orchestrated by the Cult of Kosmos to become their champion known as Deimos. Accompanied by Barnabas and Herodotos, the Eagle Bearer embarks on an extended journey across the Greek world and eventually reunites with Myrinne, who had assumed the alias of Phoenix as the oligarch of the polis of Naxos. Myrinne persuades her eldest child to convince the Spartan regime to reinstate their citizenship and ancestral estate, and continue undermining the Cult's activities in the Greek world together.
The Eagle Bearer later encounters and fights Deimos at the Battle of Pylos, but is captured and taken to Athens, where Kleon enjoys popularity as a leader of the city-state following the death of Perikles years prior. Once there, Kleon is revealed to have been a cult member all along. The Eagle Bearer successfully escapes captivity and thwarts Kleon with the help of their Athenian allies. The Eagle Bearer later joins Brasidas' Spartan forces in confronting Kleon's Athenian army at the Battle of Amphipolis, where the leaders of both armies die in battle, thus heralding the end of the first half of the Peloponnesian War. Depending on key decisions made by the player at predetermined points of the game's narrative, the Eagle Bearer either redeems or kills Deimos at the game's ending, and their actions also have a direct bearing on the fates of their extended family members and determines whether they will have a successful family reunion for the main plotline's epilogue.
Prior to the conclusion of the Peloponnesian War, the Eagle Bearer destroys the Cult's pyramid-shaped artifact and discovers that their original leader is Aspasia, whom they can kill or spare. At some point during their lifetime, the Eagle Bearer also meets their biological father Pythagoras, who is revealed to be a descendant of the Isu like Myrinne and Leonidas, and inherits the Staff of Hermes from Pythagoras to safeguard the secrets of Atlantis, gaining biological immortality in the process.
In the present, Layla encounters the Eagle Bearer, who warns her that the world needs balance between the Assassin and Templar Order ideals; either side prevailing over the other will result in the world's doom. Layla also learns that she is the prophesied one who will bring balance between the concepts of chaos and order. The Eagle Bearer gives Layla the staff before dying.
