- Kill the final target before the time runs out.
- Destroy Beacons 0/6.
- Kill Jacob Seed.
- Talk to Jacob.
The Junior Deputy is once again captured by Jacob Seed and imprisoned at the Grand View Hotel. He sees Jacob's music box outside the cage. The Junior Depuity tries to reach for the music box, but Jacob appears and stomps on the Deputy's hand. He taunts the Junior Deputy, alluding to Deputy Pratt's attempt to free the Junior Deputy. Jacob plays the music box, and the Junior Deputy goes into a psychotic fit of rage with Only You echoing in the background.
The Junior Deputy runs through the same drill, running through sections of the Grand View Hotel and St Francis Veteran's Center and engaging hostile soldiers. However, it becomes evident what Jacob has been forcefully conditioning the Junior Deputy to do. In the later section of the drill, the enemies no longer disappear into smoke but instead bleed on death. The "final target" of the drill yells "Don't shoot!" and is revealed to be Eli.
Upon killing Eli, the Junior Deputy realizes that the classical conditioning triggered them to assault the Whitetail Militia Den. Jacob appears in the hallucination and reveals that significance of the brainwashing song to the Junior Deputy - that "only you" could get close enough to eliminate Eli.
The Junior Deputy recovers from the psychosis to find Tammy in despair over Eli's death. Wheaty is in shock and pulls a gun on the Junior Deputy. Tammy holds him back and tells Wheaty that Jacob is responsible. Tammy, understanding the conditioning forced on the Junior Deputy, charges the Junior Deputy to kill Jacob or she will shoot the Junior Deputy herself.
The Junior Deputy leaves the Den to face Jacob. The initial battle involves destroying speaker stations playing Only You to remove the psychosis. With the effects of the brainwashing gone, the Junior Deputy closes in on Jacob, who is perched on a rocky outcrop with a sniper rifle. Upon neutralizing Jacob, Jacob reveals no remorse for his role as a soldier, and that Joseph had foreseen this. When he dies, the Junior Deputy recovers the key to Jacob's Gate.
$3000, Jacob's Rifle is unlocked in Shops.