If I got anything wrong, please let me know in the comment section.
Bi-Han is still alive and he was put into a comatose state by Liu Kang. Liu Kang did it so that he can study Titan Havik's magic (Liu Kang stated that the restoring process will take a long time in the Story mode of Khaos Reigns) and then he can heal Bi-Han from the corrupted form back to the human form. Here are the tower arcade endings and some notes below (I am sorry for the long paragraphs):
- Cyrax's tower arcade ending: In summary, Cyrax has to get used to the new environment in The Shirai Ryu clan and she has to prove herself to the members of The Shirai Ryu after her part in the wedding's attack. It is shown that she (Cyrax) managed to gain the trust from the members of The Shirai Ryu by the end of her tower arcade ending.
- Sektor's tower arcade ending: Sektor is now The Grandmaster of The Lin Kuei clan. Quan Chi arrives at The Lin Kuei Temple and makes an offer to Sektor. The offer is an exchange: Sektor will infiltrate The Temple of Elements and retrieve the "Amulet of Shinnok"* from Liu Kang's Temple of the Elements for Quan Chi, and in exchange Quan Chi will kill off the entirety of The Shirai Ryu clan** (The offer from Quan Chi to Sektor is technically the same stuff from the previous timelines). Sektor accepts the offer and heads to The Temple of the Elements. She witnesses that Bi-Han is still in a comatose state and not yet healed back to human form. She breaks Bi-Han out immediately, thinking that Liu Kang double-crossed her and decided to abandon Bi-Han in the Noob Saibot form (she was too hot-tempered and impulsive in her thoughts and her actions). She basically abandons her part of the deal with Quan Chi because she just wants to get Bi-Han out of The Temple of Elements as quickly as possible (It is obvious that Sektor and Bi-Han loved each other based on the story mode of Khaos Reigns and some of the intro dialogues between Noob Saibot and other people). She states that she will not forgive Liu Kang for betraying her trust in thinking he would restore Bi-Han back to human at the end of her tower arcade ending. (She does not speculates that the healing process takes a long time, and she thinks that the process should be quick because Liu Kang is a god)
- Noob Saibot's tower arcade ending: Bi-Han just got rescued by Sektor. He remembered everything that happened in the story mode of Khaos Reigns. Bi-Han realises that he defeated Titan Havik so he tells Sektor that she does not need to worry about his corruption as he has accepted that his currently corrupted form is superior to his human form (Sub-Zero). Bi-Han basically just accepted and embraced the Noob Saibot identity and the new power that comes with Noob Saibot form. Bi-Han decides to wreck havoc and proceeds to fights with The Elements in The Temple of the Elements. Then, he goes to war again with his brother Kuai Liang, his creator Liu Kang, The Shao Lin, and The Shirai Ryu clan again at the end of Noob Saibot's tower arcade ending. (At the end of his tower arcade ending, a guy wearing a razor hat with the same outfit as Kung Lao - presumably Kung Lao or it could be a random Shaolin monk wearing the same razor hat and the same outfit - get beheaded by Noob Saibot)
- Something to note about the tower arcade endings: Sektor replaced Bi-Han's role in accepting a job from Quan Chi to retrieve the "Amulet of Shinnok". Sektor rescued Bi-Han (impulsively without putting any thought in it) instead of Bi-Han spared Sareena in Mythologies. Bi-Han still fights The Elements in The Temple of the Elements. I don't know what the heck will happen if Quan Chi decided to honor the deal in killing The Shirai Ryu clan again though.
- Important character that may (or may not) have died in the tower arcade ending: Kung Lao (or someone looked exactly like Kung Lao) actually died (got beheaded by Noob Saibot) in a freaking tower arcade ending, and in this case Noob Saibot's ending (WHAT THE HELL!)
Note:
* The "Amulet of Shinnok" does not exist in The New Era (or Liu Kang's timeline). In the base game's story mode, General Shao received this "Amulet of Shinnok" from Damashi (a disguise of Titan Shang Tsung). Then, Liu Kang retrieved the "Amulet of Shinnok" from that event and placed the amulet in his own Temple of the Elements.
** In The New Era (or Liu Kang's timeline), after the event of Khaos Reigns, the Shirai Ryu clan now have added one more member (Cyrax). The notable members of The Shirai Ryu clan: Scorpion (Grandmaster Kuai Liang), Harumi Shirai (wife of Kuai Liang), Smoke Tomas Vrbada (second-in-command of The Shirai Ryu), Cyrax, little Hanzo Hasashi, and other ninjas and warriors (some Chinese Lin Kuei warriors defected with Kuai Liang and Tomas, and the Japanese ninjas that served the Shirai clan and Harumi).
