Minecraft Story Mode:Hero in Residence

The story begins with Lukas narrating a to-be-completed novel about Jesse and his / her friends' perilous adventures, including their immense popularity. As Lukas concludes, Jesse, Axel, and Olivia provide some constructive criticism regarding the novel, and Lukas agrees that some areas can be improved. Radar, Jesse's assistant, shows up afterward. The five then leave the Order's palace and go their separate ways to prepare for various Founding Day celebrations, while Radar stays with Jesse and helps him around with various tasks in Beacontown of the player's choosing, such as making a statue for Nell, and choosing which pig should be used to represent Reuben for a float. After completing them, Jesse heads down to the mines to meet Petra and puts Radar in charge for the time being.

In the mines, Jesse meets Petra and they both fight off some zombies. Petra then races Jesse through the mineshaft to find a "mystery monster", who turns out to be a llama (later found out to be named Lluna). They both eventually capture the llama, but also manage to find a strange glove atop a pyramid which whispers Jesse's name. The pyramid they are standing on collapses and reveals a bottomless pit. Acting quickly, Jesse and Petra close off the pit and escape through a hole. On the surface, Jesse leaves a sign with a warning of the player's choosing, and the two head to Champion City to bring back the llama to Stella in exchange for Petra's golden sword.

At Champion City, the two meet Stella and give the llama back to her. Stella then informs Petra that the "adventure" was a scam and that she lives in Champion City now, much to the disgust of Jesse. The two (Jesse and Petra) feel like the only way to break even is to "steal" the golden sword, and they do so by either fighting the body guards or sneaking in through the puppy kennel. The two then head to Stella's treasure room, only to notice Petra's golden sword is missing. Stella awkardly shows up, accepts "defeat", and gives Petra back her sword. As they leave, Stella informs them that this encounter was an important day in their "rivalry".

On the way back to Beacontown, the pit that Jesse and Petra covered blows up and spews out charged creepers, but the two fight them off with ease before covering it up once more. The two then head straight to Beacontown to meet with Jack, a former well-known treasure hunter, at his emporium in Bad Luck Alley. Jack talks to Jesse regarding the glove, and also introduces them to Nurm, Jack's right-hand in making maps. Jack at first refuses to help them out, but eventually accepts their offer. The four then get some armor from the Order's palace (while doing their best to ignore Radar's babbling about Founding Day preparations), and the player can choose whether or not to put Radar as acting leader while they are away.

On the way to the ocean temple, Jack informs them that the ocean monument is run by a creature known as "the Admin", who plays by its own rules. Disregarding it, the four then suit up in water helmets, swim to the ocean monument, and head inside. Inside they find some elder guardians and kill them with ease. Jesse then completes a door frame, freeing Vos simultaneously. Jack is surprised to see Vos alive, and the five make it inside the main part of the temple. Eventually, the five find the two structure blocks (the player can only choose one of the two), and fight off various Heckmouths, including "the Admin". The player can choose whether to help Petra or Jack, and the five barely make it out alive. Back in Beacontown, Jesse closes the pit with the structure block, and the five celebrate Founding Day. Just as the celebrations are about to start, the Admin goes after Jesse and vows to demolish him / her.

In a post-credits scene, Lukas is writing the novel when he sees the Admin heading for Beacontown. He quickly suits up and rides off on his horse toward Beacontown.