Stuck in a barrier maze, Soga explains that he will reach "Pandora's box" before the Major can stop him. She decides to split herself into several virtual copies and search around the maze for clues inside Soga's memory. The Major finds the day of the Qhardistani War in question. She witnesses his team slaughter the refugees as Soga explains was the 78th Composite Unit's final mission. He is shown to be ordering one of his men to give him a water bottle, which he promptly gives to one of the refugee children who drinks it and smiles at him. However, the Major sees a visual discrepancy in this memory. She attempts to tell Soga that he'd been infiltrated but is cut off of his web. VV forcibly pulls her out of the barrier maze and they both continue to infiltrate the area. Meanwhile, Batou and intelligence officer Ishikawa are shown holding up fellow Intel members before finally receiving hostage money from Home Affairs. Paz appears behind Ishikawa and tries to subdue him, but is grappled out. They fight briefly before VV and the Major arrive to take Ishikawa down. The Major infiltrates Ishikawa's mind and tells him that he's already been infected with a virus, which she decides to vaccinate. Batou meets up with Borma outside and tells him that he's lost contact with Ishikawa. He starts to escape but is stopped by Saito who shoots down his driver with a sniper. However, Batou successfully convinces Saito to join his side after promising to pay him a triple share of the amount he got from Home Affairs. Back in the Intel room, Ishikawa is also shown to change sides to the Major's team and subdues Borma in the process, who also joins them. Now with her expanded team, the Major chases after Batou along a highway. Saito comes to support Batou, shooting off VV's arm, but is taken down by an angered Kusanagi. Batou then takes advantage of a traffic control hack and manages to lose the Major's sight. She sees through the trick thanks to VV's advice and catches up to Batou, nearly eliminating him. She syncs through him and explains the truth of what happened between Soga and the refugees. The girl who he'd given the bottle had actually ambushed and shot him alongside her mother to which he killed them for. After discovering this and starting the infiltration, Soga kills himself in front of Aramaki and other operatives. The Major vaccinates Batou of the virus and promises to help him eradicate the false memories. Believing that it was over, Kusanagi is told by Aramaki that the Pandora infiltration was being sent over a new net. She discovers VV in front of her, who hacks the Major's body to the point of paralysis. VV reveals herself as an android and begins to approach the Major, but is gunned down by Batou and the Logicoma's turret. At the end, the Major releases Batou from incarceration on the condition that he join the Major's squad.

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