They trace the terrorist hacker to an underground lair, to find that he is recruiting a network of people and using their minds as a hive.
Major is hit with some stun guns and smuggled into a different part of the complex where she meets the hacker, Kuze - he tells her that they are not too dissimilar - he too went under the same procedure she did. But when they found that he was deemed to be too violent, they cast him aside and tried to have him killed.
He tells her not to take the meds so she can remember her past, before he escapes.
Major too gets away from her Hanka team and follows his advice to find the Doctor Ouelet, where she learns the truth that there were many failed experiments before her. Cutter, the man in charge, orders Major to be taken in and terminated so that they can start again.
Ouelet takes pity on her and disobeys, giving Major an address, before the Doctor is murdered by Cutter.
Major follows the address that takes her to an apartment where she meets a mother who lost her runaway daughter several years ago, and they both feel a connection.
Cutter gives the command to kill the 'Section 9' hierarchy, but they're all too tough and survive.
Major meets Kuze at the burning building in her glitch-memory, and remembers that they were runaways together, before they were kidnapped to be experimented on.
Cutter sends in a spider tank to take them out. Kuze is hit badly. Major manages to destroy the tank but a sniper kills Kuze. The Section 9 Head, Aramaki, sends in his team to rescue Major, while he confronts Cutter and shoots him to death.
Later, Major is back working for Section 9 to stop evil in the world.