Reptile returns from the Dragon King's incubation chamber in human appearance and when he finds the body of Shao Kahn he finds Baraka and Mileena and they release his spirit from the secret soul cage he kept. Shao Kahn is far too weak but Reptile is able to mislead him into gaining his trust and he gives him the sorcerers' heads and the amulet the Dragon Army was controlled by. Reptile watches in anxiousness as the events unfold and he waits for the chance to strike back at the Emperor.

Tiamat, another survivor of the Raptors, is now a threat to Reptile's plans. When Shao Kahn invaded Zaterra he fought in the battles as a general and killed many of Shao Kahn's forces. He decided the only way to survive was to flee to another realm. Him and a few others traveled back to Earth where they evolved into much stronger forces but stayed in hiding fearing Shao Kahn would find them. With Shao Kahn returning and the Dragon King fueling a burning hatred in Reptile he has no choice but to travel to Outworld and free his old friend before he can commit genocide on another race.