MK4
After his failure to take over earth through tournament battle in MK3, Kahn devises another plan to get earth. Waiting for the next tournament was just too long.
Having the ability to shapeshift, but not one to utilize this black art (it was Kahn who taught Shang Tsung the black arts of shapeshifting - a piece of info which was actually shed by Goro in the first MK movie), Kahn decides to take part in MK4 as a former and forgotten general of outworld, Reiko. He competes, but fails to secure a victory against Shinnok. (Shinnok is eventually killed by Quan Chi, who in turn later gets transported with Scorpion to the netherrealm - Quan Chi / Scorpion MK4 end video). With that, Kahn returns to Outworld, a defeated and significantly weakened warrior (MK4 Reiko end video).

Pre-MKDA
Back in Outworld, the Edenians and the Shokans had joined forces against him. Realizing that he was no match for the Edenia / Shokan alliance against his army, Kahn devises a plan that would "take him out of the picture" temporarily.
He sends Shang Tsung on a mission to locate the rogue sorceror Quan Chi, and try to gain his trust. He also sends Reptile away, but did not fill the Reptilian ninja in on his evil schemes. Kahn felt that Reptile had not earned his full trust just yet.
With that, Shang Tsung and Quan Chi finally appear before Kahn, ready for orders (MKDA intro). Kahn merely removes his helmet, and throws it on the floor, and places a body double on the floor. Immediately, all three of them flee, leaving Reptile to find a dead Kahn (but actually an imposter). (The narration by Raiden in the MKDA intro clip was actually the Thunder God's version of the story). It was Kahn's idea to make it seem as if Shang Tsung and Quan Chi had formed an alliance, and to make it seem as if he was murdered by them, when in fact the alliance was forged by Kahn himself!

MKDA
The "tournament" begins. Being "out of the picture", Kahn goes into hiding, taking his time to gather his full strength. The "Deadly Alliance" was just a distraction while he devised his ultimate plan - to use Quan Chi and Shang Tsung to revive the Dragon King's army. This would eventually allow the return of the Dragon King. And with a new found unstoppable army, the return of Kahn himself!