The CADET, a dimensional train of sorts, ferries everyone to the school. It takes a very "scenic" route, namely so that the students can be safely scanned to make sure none of the corruption from the Caldera has clung to their spirits. Once deemed safe, they arrive at Catastrophe Academy. Their first week is a whirlwind of introductions. It starts with Meloetta Melli, the combat instructor, and Salazzle Ruby, a medic for the school. There's also Blissey Sunny and Dialugia Prime, two of the school's chefs. They also learn that the CADET train was piloted by a robotic bewear named Algo Rhythm, or Algo for short. They also reunite with Proto as they go to charging stations and allow their porypsi units to recover from low-power mode. This allows the students to regain some of their unique appearance attributes. They are also given blank slate porypsi and encouraged to share their memories with them as part of their development. During this time, a virizion named Firiara and a boltund named Keraunos drop by. Firiara was once close with Savern, while Silver and Volo claim to be buddies with Keraunos. However, Firiara describes details that don't line up with Savern's world, while Keraunos has no idea who Volo and Silver are. This suggests they're from alternate universes. After recharging, the cadets meet the deans of the school: Giovanni and Giovanni. Both are mewtwo, though one has darker skin. They are the two Giovanni who showed up on the two versions of Cibus during their respective Blacklight crises. They were recruited by the Overseers and even claim to have provided logistical aid to them during the Dodra crisis. They both state that they believe friendship is the ultimate power and wish to study the power of friendship. Thus, with the Overseers help, they established Catastrophe Academy. Unsurprisingly, most of the cadets are quite suspicious of them. A few other events transpire during their first week at school... 1) After further harassment from Rosemary, Nikki goes to see Dr. Dethmettle, a witch doctor G-Max toxtricity working for the school. He reveals that, while he doesn't sense any necrozma in her, her soul is afflicted with "sandblight." He states several other students have varying degrees of sandblight, including one of two Owens, both of whom are missing (one was present during the airship flight). 2) Several students attend Reese's diplomacy class. There is talk of practical field work by having the cadets accompany Reese to negotiate with a group known as the Weavers. They appear to be a group of worlds effected by the Dodra crisis. 3) Nill shows the cadets to his home, where the recovered fragments help them access tools to augment their abilities in battle. 4) Melli teaches the cadets about Strong and Agile Styles in combat. She sets the gym up for several practice battles. 5) A handful of students are pestered by a poipole student named Quigley. He claims to be the top of the class, on account of solving several catastrophes while the other cadets were stuck in the Caldera. He has a variety of gizmos at his disposal. And he talks like a Redditor. 6) Multiple students take part in garden club, run by a shaymin named Sage. Several days later, they reveal that a lotus flower has inexplicably sprouted in the middle of the garden. 7) The students' porypsi companions awaken into memory copies of people from their lives back home. The meet up is appropriately chaotic. 8) Spear throws a slumber party for the new cadets! 9) The deans teach the students about Alliance Attacks, where they can use friendship to combine their powers in battle. 10) The students find an interfaith chapel, run by Deerling Angel. She appears to have Radiance at her disposal, however she's not in a porypsi body, limiting her abilities. She appears to be hiding something, as she encourages the students not to investigate anything about the Timekeeper that Amad mentioned. The first week comes to a head when a panicked jirachi from Flynn's home world arrives on campus, claiming the flow of time has resumed. The cadets prepare a task force to investigate the strange occurrence.

As they continue through the caverns, the cadets find three Nills banded together into a charmeleon. The Nills have been corrupted into attacking the group. Their flimsy excuse is that they want to be in control of the main Nill. The cadets battle them in a fight themed around extreme weather and emerge victorious. When they do, they seem to have a vision of the Castle General before returning to the cavern. There's another seal that the beaten Nills contain an enemy that's out to prevent them from leaving. The team rests for the day, then breaks through the seal to find the same Trio of Mind that gave them the special books they used to shore up some of their techniques. However, they've succumbed to the same glitch force as ferals the team encountered in the Caldera. They're forced to fight the Trio of Mind, whose glitched powers can disrupt the group's rhythm in battle. While this is going on, some cadets deal with a large projection that's tied to some of the crystals in the area. Another group takes off down a crystal-filled tunnel to search a nearby unexplored cavern. There, they find a mismagius who appears to be Furball's caretaker. She has three Nills in her possession, and uses them along with Furball's charm to take the zorua child out of the Caldera. She leaves behind a golurk minion that fuses with a giant crystal in the room. It's eventually taken down. And, thanks to the smaller teams' efforts, the remaining cadets defeat the Trio of Mind, who regress to inert porypsi, and the giant energized crystal that emerges from the ground. The cavern group also finds a tiny dreepy named Amad, who was taken in by Mismagius the same way as Furball. After some bickering about Amad and Furball's fate, a few cadets locate the Caldera exit, along with some faculty who'd been sent to rescue the team. They finally escape the Caldera and are boarded onto a luxury train to enjoy a nice, relaxing ride to the academy.

The next day, the team manages to break past the clockwise paths and find a divine seal at the end. While much weaker, the Cadets cannot break through, and instead hear the cries of Kecleon Trell as glitchy Paras steal his wares. After rescuing him, and finding a couple more Cadets in the process, the team regroups...

That night, strange music fills the caverns. The team investigates and meets a Koraidon named Reggie, or "Gigi," who seems to be native to the caverns. He can manipulate the crystals, transforming them into electric appliances embedded into the walls. He ordered the Cadets pizza. How nice of him! Unfortunately, he has no means of getting the Cadets out, and wishes them luck.

As the cadets expand their exploration further counterclockwise through the caverns, they started to hear distant crying. In following it, they find a sand and mushroom-filled cavern. It was a spot that several in the team previously explored by remote controlling a porypsi. Nikki takes off down a tunnel, claiming the crying is close. Not long after she disappears, a dawn wings necrozma emerges from the tunnel and begins attacking the group. She effortlessly downs several cadets, all while shouting and swearing up a storm much like Nikki does. Loud ticking is heard throughout her attack, which ends abruptly with Necrozma retreating into the tunnel. Shortly after this, Nikki emerged from the tunnel with black sand coating her fur. She claims to have no knowledge of Necrozma, having instead found a tiny ghost zorua child wedged into a crevice in the tunnel. The zorua, Furball, is familiar to a few cadets. But their attempts to calm Furball down go awry when Rosemary attacks Nikki, believing her to be the necrozma that tried to kill them. The other cadets manage to split them up and escort them back to base camp.

The Cadets find a lush cave with food and water to claim as a base camp for future exploration. However, a strange glitchy Bidoof emerges from deeper in the caverns and interrupts their rest. After being defeated, it reverts to normal. But do more of those things lurk ahead... ?

While most cadets remain in the strange cave they awaken in, a small group ends up going down the cave's lone tunnel. There, they encounter a creature similar to a void shadow, but with a starry appearance alongside red and gold rings reminiscent of a giratina. These creatures feel like a mixture of glass and rubber and make noises akin to scratching glass when nearby. After doubling back to regroup with the others, all the cadets agree to proceed down the lone tunnel together. It isn't long before they run into Nill. He informs the cadets they are inside the Caldera of Spirits and that he is unsure how they are all here or how to get out. The group also discovers that they are unable to feel the Cantus Heartbeat and, as a result, struggle to use their moves. This appears to be because their spirits are no longer occupying porypsi bodies, like during their time on the airship.