"Long ago in a distant land, I, Aku, the shape shifting master of darkness, unleashed an unspeakable evil. But a foolish samurai warrior wielding a magic sword stepped forth to oppose me. Before the final blow was struck, I tore open a portal in time, and flung him into the future where my evil is law. Now the fool seeks to return to the past and undo the future that is Aku."
But what Jack didn't know was that the future Aku sent him into was an alternate future. In it not only had Aku conquered the world but also gained the ability to travel to different dimensions and uses warriors from these dimensions to build up an army. With this army he rules over the future with an iron fist.
In this future a young Bruce Wayne watched his parents get gunned down by Aku's henchmen robots. It was then that he dedicated his entire life to ridding the world of Aku's evil. So he became Batman and fought against Aku's rule. But over time he got old. He knew he would not be able to fight any more and looked for a successor. It did not take time for him to find Terry McGinnis. With Terry by his side Bruce set out to form a resistance against Aku's army. Over time Bruce enlisted two of the world's best scientists for aid. With the help of Dexter they were able to build a machine that would allow them to go to other dimensions and enlist other warriors to their cause. Soon their resistance army grew to include characters such as Ben Tennyson, Snake-Eyes, Cole McGrath, Sora, and others. With another scientist Bruce began working on a separate project that not even Terry knew about. Over time Terry's army did what they could but nothing they tried would destroy Aku. No, there was only one weapon in existence that could finally destroy Aku. A weapon that just so happened to be in the hands of Jack.