The two schools both existed at one point, with Naranja being an older school focused on social studies, history, and arts, while Uva is a somewhat newer school focused on STEM. The two schools were in talks of a merger for awhile. Naranja is the school that had the bullying incident that led to a mass resignment of staff, which turned into the two schools merging into Uva. Both school uniforms are currently permitted, with the orange being associated with arts students and purple with STEM students.
Nemona is sent to meet Luz, a foster child that moved in near her recently, and introduce her to the academy. Picking a Pokémon, meeting Koraidon, and meeting Arven happen as usual.
Ezl was a student who transferred in late the previous year, but quickly took to the top of the grade, being perfect in everything except fine arts. His unusual demeanor gets him targeted by Star grunts alongside Penny.
Luz does the league path with Nemona, Ezl ends up on the herb path with Arven, and both are involved with Star.
Ezl follows Arven around as he realizes Turo is his father and he’s trying to figure out how to get to Turo and the time machine. And then finding the herbs helps to cure whatever is wrong with Miraidon… it should be noted, Arven had no idea that there’s a Miraidon around until Ezl lets her out.
While most things pulled through the time machine ended up in Area Zero, a few missed the mark per se, and ended up where they shouldn’t (see: Sandy Shocks and Iron Jugulis canonically being spotted around Paldea, and Iron Treads roaming around the desert). This is how Luz and Ezl have no idea where they are or what happened.
Koraidon is the canon partner (beta) Koraidon. Miraidon is Ezl’s, and her getting pulled into the time machine is what got Ezl pulled through as well. While the two were pulled through together, they were separated (Ezl ended up on the surface, and Miraidon in Area Zero). She and Koraidon got into a fight, Turo got killed, and both fled the scene. Koraidon moped around injured for awhile until Luz found him. Miraidon was able to seek out Ezl pretty fast (him being the only android around probably made sensing easy, lol).
Being near the AI-enhancing crystals in the chamber in Turo’s lab don’t do good things to either Ezl or Miraidon. This allows for the Guardian of Area Zero fight to happen.