I've finished pretty much every Klassic Tower ending bar Shinnok's, and some of them add up to a story. That is, if you discount certain things and pay attention more to the narration than the pictures. Obviously, there's spoilers for pretty much every Klassic Tower ending from here.
After the events of the story (but not the epilogue- I'll get to that in a minute), Kotal Khan hires Erron Black to kill the SF four (Cassie, Jacqui, Takeda and Jin). However, Jax is around with them due to Cage asking him to take over whilst he's in hospital, and successfully kills Black, but dies in the attempt. Sonya foresees it in a dream and is told by Johnny. This event shakes up several of the heroes. Kung Jin decides to travel to the Netherrealm to attempt to aid Kung Lao, despite Raiden saying it wouldn't work. Takeda decides it's now or never to kill the assassin who murdered his mother, and takes Kenshi with him, ending up meeting Taven and killing Daegon. Raiden, corrupted by Shinnok and further motivated by Jax's death, decides to go after his threats. He sends Jacqui to spy on Kotal, where she takes the golden skull, and sends Cassie to kill Shujinko so the events of Deception can't take place. He snaps Scorpion out of his suicidal state and infused him and the Shirai Ryu (minus Takeda, who is in the middle of hunting down Daegon) with a portion of the Jinsei, in order to bring him along to invade Outworld. Down in Outworld, things are dire. Erron is dead, Shang Tsung has been revived from, and has killed, Ermac, and is making an army of Mileenas in his flesh pits. Reptile has left to his new raptor clan after being sent on a scouting mission and Ferra is now a brute in the process of being sold off to a new rider. Without any forces to speak of, and with whatever artifact he had being stolen by Jacqui, Kotal is defeated by Raiden, and has to plead to the Elder Gods to give him a chance, and invokes a new Mortal Kombat tournament for the fate of Outworld. And finally, with the Lin Kuei left to defend Earthrealm alone (since the Shirai Ryu are in Outworld), Sub Zero finds the frost dragon to make them more powerful.
Liu Kang took control of the Netherrealm before Jax died. Just before he left to attack Outworld, Raiden cut off Shinnok's head to make a point to Liu and Kitana about invading other realms, as they both appear to be ruling the Netherrealm together at that point. At the very least, Liu Kang's story is already proven canon by the epilogue to the story. Kitana's vision, given by whatever being killed Jade in 9 that apparently wants to restore the unaltered Armageddon timeline, happened afterwards, otherwise she'd have told Raiden to stop meddling in the timeline.
This story assumes that the dead Quan Chi and the defeated D'vorah's Klassic Tower endings aren't canon. It also does not account for Shinnok's story, nor the image at the end of Khan's story which breaks the canon as Ermac, Erron, Ferra/Torr and Reptile all appear in it. It's just a headcanon of mine, but it would be very interesting if such a broad range of endings were actually canon. It definitely sets up the next game in an interesting way.