The world was saved. Everyone got a happy ending and Beacon town could live to see another day. After the events of Minecraft Story Mode Season 2, everything should have a nice bow wrapped up on it, right? That is not the case for the realms and the portal hall though; as an old threat arises. The Old Builders have been biding their time, plotting revenge and seeking control of the realms. With their plan laid out and their forces strong, they are more dangerous than ever. With the "New Order of the Stone" split up and unprepared, a new order will have to rise and save the world.

In the land of Ninjago, the Ninja add a new member to their team. However, with new friends come new threats in the form of Kranus, a former servant of the Overlord who seeks revenge on Ninjago and nothing will stop him. With limited time on their hands, the Ninja must train Matt, the new Ninja, and help him unlock his true potential if they are to stop Kranus and save Ninjago before it is too late.

Ezra Bridger is a Jedi knight who has gone back in time to the end of the Clone Wars and the Jedi Order. After an attempt to stop Order 66, he ends up as a man trapped in time. Now he must work his way back to the present with his vast knowledge about the future; he must change the timeline as little as possible to his favor if he is to survive.