In the final round of the Battle Arena Toshinden tournament, Eiji Shinjo faces the tournament's sponsor, Gaia, in Mortal Kombat. Gaia mentions that Eiji's skills are comparable to those of his long-lost brother, Sho, but before he can explain, the fight is interrupted by a man called Chaos, who works for the same Organization as Gaia and has been sent to eliminate him upon discovering that Gaia is rallying fighters to overthrow the Organization.

Eiji and Kayin meet up with another competitor, Ellis, and warn her of the danger. Believing she may be slain, Eiji and Kayin set a trap for Chaos and surprise him when he arrives.