In Story Mode, Sonya Blade announces to Cassie Cage, Johnny Cage, Jacqui Briggs, and the Special Forces that Jackson "Jax" Briggs has retired, and therefore, Cassie, Sonya and Johnny's daughter, is promoted to Commander, but not before passing her final test against her mother in kombat.
After old Johnny teaches his younger self a lesson from disrespecting past Sonya, the base is attacked by the Black Dragon and the Cyber Lin Kuei. The two Johnnys put differences aside, and fight back against the Black Dragon, before the younger Johnny is grazed on the cheek by a bullet, causing a faded scar to appear on the same spot for the present Cage. Driven into a rage, the younger Cage charges headlong into the melee, firing wildly and pushing back the Black Dragon henchmen, leaving his older counterpart to deal with the past Erron Black, who is still affiliated with the criminal group. Johnny questions the gunslinger's allegiance, since his present counterpart remains in a tenuous alliance with Earthrealm by virtue of staying in Kotal Kahn's service. Black responds that he always picks winners, to which Johnny counters that he chose poorly after defeating him. The elder Cage finds Cassie, alive but injured, who informs him that past Sonya has been captured. Johnny heads out to rescue her, comandeering a tank on his way to deal with the Cyber Lin Kuei.
- Johnny Cage can be seen in the background cheering while standing.
- If you play as or against Johnny Cage on this stage, he will no longer be present in the background.