In Konquest, Tanya is on Shao Kahn's side holding Sindel. Edenia is at war with Outworld. We knew that since Deadly Alliance. Well, I think I got a bit of history.
All of Shinnok's men went to Shao Kahn when Shinnok went out.
Tanya is the main example.
She's lived in Edenia her whole life, right ? she's the ambassador's daughter. However, she gets a call from someone named Shinnok. Now, Tanya has always been a bit power hungry, so she agrees. She tells Sindel that refugees want in on Edenia since the Netherealm is free now. Sindel orders that they open a portal to let them in. However, the refugees are all actually Shinnok and his Army of Darkness in disguise. Soon, Kitana and Sindel are taken captive and Edenia is under Shinnok's control. Tanya is made apart of Shinnok's army. Her next mission is to derail the Earthrealm warriors. She does, by pretending to ally with them, show them around.
However, eventually somehow Tanya is found out. When the bad guys are defeated, Tanya merely runs away, knowing there's no reason to stay since her master is defeated and Edenia will probably want her executed or imprisoned. She isolates herself in Outworld.
She eventually meets Shao Kahn, who is starting over. She decides to join him, since his army is powerful and at war with Edenia. She wants power, as always. Her mission is to join Outworld warriors to infiltrate Edenia. She does, and she kidnaps Sindel, watching over her until further orders. However, Shujinko comes and takes her out (for his own reasons), rescuing Sindel.
Tanya is freaking out, knowing she could be punished. But to her relief, she finds Shao Kahn dead, and the Deadly Alliance were now the controllers of Outworld's armies. They decide to keep Tanya and ask her to lead their armies into Edenia. She is willing to do so, but never gets to. Soon, the palace is destroyed by Raiden's blast and Tanya has no master.
She wanders Outworld, really missing her hometown of Edenia. Eventually, Baraka comes to her and tells her to serve Onaga or she dies. Tanya agrees, loving her life.
Also, think about it. Reiko is Shao Kahn's greatest general ? He was Shinnok's general. Something tells me after Shinnok died, Reiko employed himself to Shao Kahn.
I think most of the baddies from MK4 went to Shao Kahn once Shinnok died. Fills in alot of plot holes, IMO.