After the events of Series 12, the Thirteenth Doctor managed to escape from her prison. Separated by her companions, she crashed with the TARDIS on Earth, triggering a regeneration. The Doctor, now regenerated as brown-haired teenage boy, must travel across an Earth destroyed by the Tragedy, and try to restore Hope.

The adventures of the Sixteenth Doctor continues, as he travels across Time and Space with Angie and Akane. But, soon, they'll start noticed that the very fabric of the Multiverse is in danger.

Natsumi and Hajime are students at Hope's Peak Academy Reserve Course, one day, Natsumi was saved from an alien disguised as one of her classmates by Nagito Komaeda, the "Super High School Level Lucky Student" of Class 77-B. After him and Hajime came to save her, Nagito reveals that his identity is false. In reality, he's the 16th reincarnation of an alien called "The Doctor".

Everything is lost, Chiaki Nanami, Hope's Peak Academy Ultimate Gamer, was going to find one of her classmates that disappeared. Unfortunately, a Renegade Time Lord known as "the Master" brainwashed all of her classmates to become her puppets. Now, Chiaki was going to face her demise, unable to do anything to save them. This was truly her worst day ever.

Hajime is wondering if he has a crush on Natsumi and should confess to her, but he's scared as hell. So the Doctor, trying to be a wingman, decides to bring the to an amusement park planet to set the athmosphere. Things will not go as planned. (Valentine's Day Special to Doctor Nagito)

The mastermind was revealed, her lies exposed. But the survivors aren't ever returning to normal life again. Despair is still around the corner of the Doctor...