"The Admin" meets Jesse at Beacontown, and the two fight against each other, after changing time from day to night and destroying part of Beacontown in the process. "The Admin" also takes the structure block away from Jesse and swallows it whole. Just as "The Admin" is about to swallow Jesse whole, Lukas distracts him with a bow to the eye, and saves Jesse from certain death. Jesse then realizes that the symbol on "The Admin's" head was the same symbol shown on the Heckmouths back at the ocean temple, and Jesse realizes that destroying the symbol is the only way of destroying "the Admin". With no time to spare, Jesse takes Lukas' horse, climbs up "the Admin", and kills it, dropping a giant clock in the process, which Jesse uses to make the sun come up.
In the aftermath, Jesse and others are doing all they can to rebuild Beacontown, and Jesse can choose whether to give Lukas or Radar the title of "Clockmaster", which basically involves watching a giant clock all day. Jesse then meets up with Jack and Vos, who unintentionally spill that they are about to go on a new adventure with Nurm and Petra, much to the disgust of Jesse. Suddenly, Jesse and Petra see snowflakes falling in Beacontown, and one of them ends up melting inside the glove, revealing "the Admin" to be a snowman. The snowman then gives Jesse a challenge: Beacontown will remain dark and huddled with hostile mobs until Jesse reclaims the giant clock, which the snowman says is "at the tippy top of my awesome, fantastic, super-deadly icy palace of despair". Jesse and numerous others fight off numerous strays and zombies, and the group (consisting of Jesse, Petra, Lukas, Radar, Jack, and Vos) head toward the ice palace. On the way to the ice palace, the group encounter Lluna and Stella, once again talking about their "rivalry". The group ignore her, and she eventually tags along with them in order to "keep an eye on them". Stella then reveals that Radar was originally part of Stella's inventory management team, and insists that Jesse be careful about Radar having too much leadership.
At the ice palace, the snowman drops the group into the pit, and Jesse can choose whether to go with Lukas or Petra in order to find the clock. The group eventually end up in a roller-coaster-like maze, and meet the snowman once more, giving the group (consisting of Jesse, Lukas, and Radar or Jesse, Petra, Jack, and Vos) several challenges, such as a shooting gallery, parkour, and a fight with a giant snow golem. Nonetheless, the Admin insists that only one person is supposed to win, and throws Radar into another challenge, with Vos randomly disappearing. The group then mine their way out with a diamond pickaxe and face numerous Endercreepers. Jesse can then choose whether Petra or Jack should get the clock, and whether Stella should come along or leave her be. Jack makes it up to the clock and destroys it, turning the world back to normal time. Jack insists on finding Vos, and the group help Jack find him. Suddenly, it is revealed that Vos is indeed the Admin, and he insists on partnering with Stella (only if the player decides to let her come along). The Admin then teleports Jesse to a jailhouse.
In a post-credits scene, the warden tells the player that the Admin sends people here that they have "special plans" for them, and that the people are "not very nice, either". The scene then cuts to Prisoner X laughing malevolently.