Having lost consciousness, Vincent awakens in a tube in the WRO headquarters being watched over by Shalua, who Vincent briefly mistakes for Lucrecia. After recovering fully, Vincent is given a new task by Reeve: go to the Shinra Mansion in Nibelheim to find as much of Lucrecia's thesis on Chaos as possible. As well as the possibility of Vincent's Chaos form giving the WRO a fighting chance against Deepground, Shalua has a suspicion of Deepground's ultimate goal having something to do with the final WEAPON, Omega. Suddenly, WRO security is breached by Deepground soldiers led by Azul. Fighting his way through the complex and aiding WRO soldiers, Vincent finds Shalua, who sees that Vincent has been followed by the girl who was accompanying Azul earlier. After shedding her camouflage, the girl is revealed to be Shelke, Shalua's long-lost younger sister and the "reason to live" she had told Vincent of during their first meeting. Shelke reveals that she remembers being captured by Deepground, and that the Mako infusions they used to keep her in a 10-year old body (she is actually 19) are now required to keep her alive. Despite this, she still tries to complete her objective, and tries to attack Shalua. Fortunately, Reeve intervenes. Using special tranquilizer bullets, Vincent is able to best Shelke in battle and sedate her. However, upon leaving, Azul ambushes Vincent, showing that Shelke's attack was merely a foil for his own. By using nearby explosive barrels, Vincent is able to defeat Azul despite his shielding. After dealing with the problem, Vincent makes for Nibelheim to find Lucrecia's reports on Omega WEAPON and Chaos. Reeve advises him to go through the sewers, as the path above ground is crawling with Deepground soldiers.
Reaching the mansion through the sewers, Vincent is surprised to find a hologram of Lucrecia waiting for him, apologizing again. After finding the remaining data, Vincent runs into Rosso again. Preparing to battle her, Rosso instead flees and sends a spider-like mecha, the Black Widow, after him, which Vincent destroys in the mansion foyer. Preparing to leave, Rosso ambushes Vincent and plunges her hand into his chest, retrieving the Protomateria, which is revealed to be what allows Vincent to control Chaos. Without it, it is possible for Chaos to overwhelm him. Finally, Rosso makes to kill Vincent, but a sudden flash covers Vincent's rescue by a mysterious figure.