The story begins with Kratos on the tallest cliff in Greece, lamenting that the gods have abandoned him; hopeless, he consigns himself to the waves below. The story then rewinds three weeks into the past; as the game progresses, it also relates Kratos' past through numerous flashbacks. For reasons of simplicity, this summary covers all of these events in chronological order.
Kratos is a fearsome Spartan warrior, unmatched in strategy, tactics and ferocity; such was his success that his original fifty-man group grew into an army of thousands. However, in a battle against a barbarian horde, his army was massacred, and, in desperation, Kratos offered his life and service to Ares, the God of War, in exchange for salvation. Ares, sensing enormous power in Kratos, accepted his offer and destroyed the barbarians. He also granted Kratos the Blades of Chaos, whose chains are seared to Kratos' arms. Kratos, now Ares' servant, led his Spartans in conquering much of Greece.
In his final battle, Kratos' army came across a village that worshiped Athena and put the residents to the sword. Despite his own foreboding feelings and the warnings of the local oracle, Kratos personally entered the village's temple and slaughtered all within. Unfortunately, after his blood-lust cleared, he realized that his two last victims had been his beloved wife and daughter; Ares had engineered the battle to sever the last of Kratos' humanity and turn him into a perfect warrior. Despite this, Kratos renounced his service to Ares and began to wander the Aegean, lamenting his deeds and serving the Olympus for ten years in exchange for redemption from his deeds.
The player becomes involved in Kratos' story as he is approaching the city of Athens, under siege by Ares' army. After a battle with the QueenHydra, Kratos moves into the city and attempts to save it at Athena's behest, having been promised full absolution if he succeeds. He fights his way through the attacking forces to find the Oracle of Athens, and learns from her that only Pandora's Box can give a mortal the power to kill a god. Unfortunately, due to the gods' fear of this object, the box is locked deep within the Temple of Pandora, a murderous edifice constructed on the back of the Titan Kronos, who wanders the Desert of Lost Souls.
Kratos makes his way to the Temple, defeating many foes and evading the many traps built into the Temple, and recovers Pandora's Box (a process that contains most of the game's content). However, as he pushes the Box out of the Temple, Ares senses his success and slays him with a thrown pillar. Kratos, despite this, is able to escape the Underworld and return to the mortal realm, conveniently in Athens, where he regains Pandora's Box and confronts Ares.
When Kratos wins their opening exchange, Ares attempts to drive Kratos mad by making him relive the death of his family. Ares traps Kratos in an illusion of that ill-fated temple and then forces him to defend his family against murderous copies of Kratos himself. When Kratos succeeds, Ares strips the Blades of Chaos from Kratos' arms and impales Kratos' family with them before dissolving the illusion. Freed from his own mind but now weaponless, Kratos is at the mercy of Ares until he spots the Blade of the Gods, serving as an ornamental bridge inside Athens. As he pulls it out, he engages in a sword battle with Ares. After being defeated, Ares reminds Kratos that he helped him in his time of need and then told him he was trying to make him a great warrior. Kratos responds: "You succeeded", then proceeds to runs Ares through with the sword through his neck and chest. Ares collapses, and dies in a massive explosion.
After receiving congratulations from the Gods, Kratos asks Athena to remove the nightmares of his past. Athena explains that the gods can only forgive him for his sins; the nightmares are beyond anyone's power to remove. Feeling abandoned, Kratos climbs to the bluffs overlooking the Aegean Sea and tosses himself over the edge, bringing the story full circle. However, as he plummets through the waves below, he is pulled out by Athena. He has served the gods well, she explains and the Gods cannot allow to die one who has done them such a great service, and there is a throne on Olympus that lacks an occupant: the one belonging to the God of War...
After his defeat of Ares, has become the New God of War, but has not been accepted by the other members of the Greek pantheon due to his ruthless conquest of The Greek City-States. He finds enjoyment the only way he can, by leading his Spartan army in conquering Greece. The game begins as he descends to Rhodes, where an eagle(Zeus)robs him of some ofhis godly powers, and brings to life the Colossus of Rhodes, which comes to life and attempts to kill Kratos. After a protracted conflict with the bronze giant that rages across the city, Zeus offers Kratos the Blade of Olympus, which Zeus himself used to overthrow the Titans, who were led by Zeus' father Kronos. At Zeus' behest, Kratos infuses the blade with his own godly power, rendering him mortal but rendering him victorius. Unfortunately, Kratos is severely wounded as he boasts to the gods by the Collossus' hand in the battle-and Zeus, having engineered the entire plot, demands that Kratos swear allegiance to him. Though weakened and unable to fight back, Kratos defies him, and is slain by Lord of Olympus.
However, as Kratos is being dragged into torment in the Underworld he is saved by Gaia, one of the Titans, who has observed his life up to this point and offers to save his life and help restore his powers. When the Titans were defeated by the Olympians, they were punished and humiliated, and they want Kratos' help to exact revenge. Kratos escapes the Underworld and is bidden by Gaia to find the Sisters of Fate in order to change his past; she then gives Kratos the aid of Pegasus to traverse the distance to the Fates. Kratos and Pegasus fly to the Island of Creation where the Sisters of Fate await, well guarded on both the air and on land. Along these travels, Kratos encounters a number of Titans and defeats many heroes and monsters, gaining new powers, weapons, and magical abilities to replace those lost to Zeus (as in the previous game, this process comprises the bulk of gameplay).
Kratos finally confronts the Sisters, Lakhesis, Atropos, and Clotho, who operate and defend the Loom of Fate, which rules the lives of mortals and gods alike. Though they try everything at their disposal, including attempting to change the outcome of the first game's final battle, Kratos defeats them all and gains control of the Loom. He first goes back to his death at Zeus' hands in Rhodes, leading to a lengthy battle with the King of the Gods. In which Kratos is victorius, but when he is about to strike the deathblow, Athena interposes herself, saving her father at the cost of her life. Her dying words reveal that Zeus' actions are meant to break the cycle in Olympus of son killing father, by killing Kratos (the son) before he can kill Zeus (the father). Kratos then vows to exact retribution on the Gods of Olympus for their petty acts of self-preservation.
Returning to the Loom, which is now collapsing, Kratos uses it once again to go further back in time, into the original war between the Gods and Titans, and offers the Titans the chance to come to the present day, where Zeus is weakened and Olympus in a state of confusion. Thus, the game ends with the Gods of Olympus, in the present, watching in horror as the Titans climb Mount Olympus, led by Kratos.