The story is told mostly in a large flashback, starting from the present where Kratos, standing on top of the largest cliff in Greece, laments how the Gods have abandoned him, and then tosses himself into the waters below.

While the player starts the game three weeks prior to this event, Kratos' background is told by the Narrator during the game (revealed to be Gaia in God of War 2). Kratos was a fearsome Spartan warrior. His ferocity in battle lead him from leading just 50 men to an army of thousands. However, in a battle against a large barbarian horde, his army faced a massacre, and in a desperate measure, Kratos offered his life to Ares, the God of War, in exchange for Ares to smite down his enemies. Ares sensed the making of a God in Kratos and granted him the Blades of Chaos, made in the depths of Hades, the blades were attached on long chains to Kratos' arms, Ares then wiped the barbarian forces out, with Kratos decapitating the leader.

Kratos then became Ares' servant, leading the Spartan army in conquering much of Greece for themselves. In one battle, they came across a village that worshiped Athena, and began to kill all in the village. Despite his own foreboding feelings and the warnings of the local Oracle of the village, Kratos entered the temple of Athena, slaughtered all the survivors inside and set the building aflame in his bloodlust. Suddenly, he realized that his two last victims were his wife and his daughter; Ares apears in the flames and admits he used this as a test of Kratos' power and to remove the last vestiges of his humanity so he could become death itself. The village Oracle cursed Kratos binding the ashes of his dead family to his skin, turning him ghostly white as a reminder of his horrible deed, leading to him being called the "The Ghost of Sparta". Kratos renounced his service to Ares and began to wander the earth, lamenting his deeds, while serving the remaining Gods of Olympus for ten years.

The player becomes involved in Kratos' story as he is approaching Athena's city of Athens under siege by Ares' army three weeks prior to the opening scene. After defeating the giant Hydra, he comes ashore and is approached by Athena, who sees Kratos' potential to stop Ares and save her beloved city. Kratos fights his way through the attacking forces to find the Oracle of Athens. After saving the Oracle from falling to death, she tells Kratos that the only way to stop Ares is to retrieve Pandora's Box that is located deep within the Temple of Pandora, built on the back of the Titan Kronos that wanders the Desert of Lost Souls.

Kratos battling Undead Legionaries

Kratos is then met by Athena on the outskirts of the desert and is told he must kill three sirens to find the way to Kronos. After doing so and climbing aboard, makes his way to the Temple, defeating many of the foes and near fatal traps built into the Temple by its crazed architect, and recovers Pandora's Box. Athena appears again and demands that Kratos returns to Athens. Ares however also senses his success, and throws a pillar from Athens to the Temple, impaling Kratos on a wall and killing him. However, Kratos is able to escape the Underworld and return to his mortal body, helped back up to earth by the mysterious gravedigger encountered earlier on. With the power of Pandora's Box, he returns to Athens to gain his ultimate revenge against Ares.

Ares after being injured in their first duel, first attempts to drive Kratos mad by making him relive the moment of the death of his family at his own hands. He creates copies of Kratos and makes them attack his wife and child. But Kratos is able to kill them and seemingly save his family. However Ares strips the Blades of Chaos from his arms and impales his family with them. Kratos is anguished by this. He leaves this memory and is almost killed by Ares until he spots a huge sword used as a bridge from a statue of Athena to Athens. This is a giant replica of the Blade of Olympus, and Kratos grabs it and engages his former master and once Saviour in a final sword fight. After Ares is defeated he desperately tries to remind Kratos how he saved his life and his plans to make him the ultimate warrior. Kratos shows no pity and after declaring he's now the great warrior Ares envisioned, impales the god through the chest. Ares is destroyed in a colossal explosion.

While receiving the 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, unfortunately, are permanent. No God or mortal could possibly forget them. Feeling abandoned and hopeless, Kratos climbs back to the Bluffs overlooking the Aegean Sea and as the game comes full circle, tosses himself over the edge. However, as he breaks the waves below, he is pulled out and placed back on the cliff by Athena to the heights of Mount Olympus. He has served the gods well, she explains, and there is a throne waiting for him that currently has no occupant - the throne of the God of War.