After being defeated yet again by the protagonists, they proceed to use C-4 and their ammunition to destroy Phobos and Gestalt once and for all.The final boss in Titan Rune dungeons will drop one Sidereal Essence. After losing his sixth and final Corpus, Jesus/Christoff attempts to banish him back to the Other Place, only for Phobos to rebuttal that he will merge himself, Gestalt, and the Other Place together and become a god, and then possesses Gestalt. After losing his fourth Corpus, Phobos will steal Jesus/Christoff's halo for himself, and become more powerful than ever, repeating his previous phase at a faster rate. During his first phase, Phobos will teleport around to player to attack, during his second and third phases, he will throw debris at the player, summon souls, use a sword to attack the player, and discharge anyone too close to him. The player must destroy 'Corpus Bars' to damage him, to which he will teleport out of the arena and summon souls from the underworld to attack the protagonists. After the fight is over, and Gestalt is defeated, Phobos is released from Hell/the Other Place and attacks the protagonists himself. He controls a resurrected Mag Agent: Gestalt to fight Hank, Jesus/Christoff, Sanford, and Deimos. Phobos makes his return in the last level of the game, 'The Rush', as one of the final enemies in the entire game. He also sent a message to the Sheriff mentioning Dr. A statue of Phobos in a powerful stance is seen, raising his binary sword into the air.

Phobos serves as a posthumous influence throughout most of the game, as the Nexus Core continues to obey his orders even after his death. Once he is killed, Jesus will say to him, 'Goodnight, Phobos'. Despite his evasive skills, he is still vulnerable to Nexus bolts and cannot block them with his sword. When he is using the TMP, he dodges attacks by performing very high back flips or utilizing his TAC-Bar. While wielding the binary sword, he uses it to block attacks.

He doesn't reappear until the final level, where he resides in the last room armed with the binary sword and a TMP. However, once he is successfully hit by an attack, he will flee the room and tell Dr. Using the binary sword, he can deflect almost every bullet fired at him and knock out any melee weapons used against him. Christoff when he discovers he has defected from Project Nexus. Phobos first appears in level, wielding only his binary sword and confronting Dr. Phobos serves as the posthumous overarching antagonist of Episode 1, and the main antagonist of Episode 1.5. Biography Madness: Project Nexus (Classic)

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