Mehem (Idon't know why I make these story analyses, but I like them.), Jax's Story...
Special Forces
Jax wears some prototype arms in this game. He initially gets a report about the Black Dragon breaking out, and decides to investigate. What he finds does not please him: his squad was killed. Jax then swears vengance on the Black Dragon and hunts down the many escapees. When he encounters Kano, he finds himself in Outworld. In the end, Kano was beaten, and Jax ditches the arms.
MK2
When Johnny Cage crossed Special Forces territory, Jax nabs him and interrogates him on the whereabouts of Sonya and Kano. Cage tells Jax that they are in Outworld.Jax decided to believe Cage and goes to Outworld to find Sonya and Kano. Although he did not win the tournament, he did free Sonya and Kano, even though Kano escaped eventually.
MK3
This is the first official installment where he gets the metal arms. Upon returning to Earthrealm, Jax and Sonya try to convince the US government to prepare for the Outworld invasion. The plea fell on deaf ears. Jax becomes one of the few souls Raiden proected when Shao Khn tries to fuse Earthrealm with Outworld. His side manages to win and, as a result, the Outer World Investigation Agency (OWIA) is formed with the goal of protecting the Earth from various interrealm threats.
MK4
Jax again joins the good guys when he learns that Sonya was in Edenia during Shinnok's attack. He manages to survive and, while at it, take out Jarek (Or so he thought) and repair the Lin Kuei Cyborg Cyrax and find his soul.
Deadly Alliance
When Cyrax and Kenshi, both mambers of the OWIA, go missing, he started getting concerned. When the Red Dragon Hsu Hao (Who joined the OWIA under Mavado's orders) bombs the OWIA facility, Jax swears vengance. He met up with Raiden, Sonya, Johnny Cage, Bo' Rai Cho, Sub-Zero, Frost, Kitana and Kung Lao on Shang Tsung's old island and departed to face the Deadly Alliance.
Unchained
Unfortunately, Jax and most of his allies (Bo' Rai Cho stayed behind and Frost betrayed Sub-Zero) were killed in the fight and was resurrected by Onaga to serve him. Eventually, with the help of Ermac and Liu Kang's Spirit, he and his allies were freed, and Jax develops a vedetta against Onaga. Out of the four new additions to Unchained, his ending is the only non-canon ending. It stated that Jax beat the living crap out of Onaga, propelled by anger (his vendetta, maybe?) and brutally impaled Onaga with the Netherrealm Kamidogu.
Armageddon
Even though Jax's bio is unreleased, Sonya's explains what has happened. Jax was deployed to investigate the crash of a Tekunin warship. At first, everything seemed fine until the bioscanners on his arms displayed odd life signs until they wiped out entirely. Snya assumes that he was kidnapped by the Tekunin grandmaster, Sektor. His ending states that upon defeating Blaze, Jax transforms into a full cyborg. Jax then notices a mind-control chip in him and kills it's implanter, Sektor. Nobody knows if he will return to the Special forces.
