I agree with [MENTION=11230]Guyver Spawn[/MENTION] about how MKX will pick up. It will be revealed that Liu Kang is alive and he will spend the first part of the story unconscious, being somehow preserved from death. Given that Shao Khan's pact with Quan Chi is still in effect, if Liu Kang were to die from injuries sustained during the invasion, he would become another thrall of Quan Chi.
Back at what remains of Special Forces headquarters, Raiden's power alone is not enough to restore Liu, just as Shang Tsung's wasn't enough to heal Kabal's damaged lungs. Raiden, Sonya and Johnny need to search for a way to either bring Liu out of his coma or nullify Khan's pact with Quan Chi (ie by ending Quan Chi). They hope to achieve the first objective before having to resort to the second.
The three warriors plan an attack on Lin Kuei headquarters, knowing that it may hold the only technology capable of restoring Liu. With much of Raiden's power being diverted to Liu's life support, he can accompany Sonya and Johnny as a projection only, unable to aid them in battle for now. Meanwhile, Johnny begins experiencing destructive and uncontrollable energy surges, just as we saw in his arcade ending.
Raiden's teleport was way off the mark this time, leaving Johhny and Sonya to infiltrate the Lin Kuei on foot. Unfortunately, they're not alone. Khan's remaining forces (Mileena, Reptile, Goro, Sheeva and Kintaro, only Ermac and Kano are missing) have converged on the assassins' stronghold, knowing its advanced technology is their only hope of returning to Outworld. The three heroes bypass the security perimeter to find the Shokans gaining ground against Sektor's cybernetic soldiers. Mileena and Reptile have beaten Cyrax into submission and turn their attention to Sonya and Johhny, finding that Raiden is untouchable.
With Johnny's power surging, it's up to Sonya to defeat them. She battles fiercely but they gain the upper hand when the Shokans join the fray. Things look grim, but Cyrax has awakened. Seeing that the threat to Lin Kuei headquarters will not relent, he self-destructs amid the chaos and the last of Khan's forces seem to meet their end.
When they reach the Lin Kuei's portal, they find it guarded by Sektor with his remaining soldiers and a warrior who appears to be Sub-Zero. The three heroes, particularly Raiden, are shocked to see their former ally again. As he advances towards them with Sektor however, he blasts Raiden with a dark cloud of what seems to be Netherrealm energy, banishing the thunder god's projection and leaving Johhny and Sonya to face their foes without his guidance. Bi Han has returned.
The two fight valiantly against Sektor and Sub-Zero, until Johnny suffers another surge and the battle seems lost. Before the Lin Kuei warriors can land their fatal blows, they are knocked aside by a flash of green light. As they regain their composure, Ermac positions himself between them and their victims. 'We sense the means to leave this realm. Deny us at your peril, Lin Kuei.'
Meanwhile in Edenia, Rain has maintained a tenuous grip on power since Khan's defeat separated his realm from Outworld. Confidently, arrogantly, he allows himself to become complacent for just a moment. One moment is all it takes for the power-hungry daughter of an Edenian aristocrat to make her move. Tanya's plans will soon come to fruition when the sorcerer's portal opens, just where he said it would. Unfortunately for Rain, the refugees and reinforcements he was expecting are not all this portal will be bringing into his realm.