To break down the overarching plot, I will start with some basic timeline info:
I headcanon that HA/LL are first years like Makoto's class.
PK/PM are second-years like Hajime/the cast of DR2.
And M4/RD are third-years like the cast of DRV3.
I had it in mind that every character of every aforementioned game was a student at Hope's Peak, divided into one of the three aforementioned years.
The Tragedy begins in Makoto's first year/Hajime's second because that is when Junko reaches Hope's Peak and causes chaos for the rest of Hajime's cohort.
During the course of that year, expansions were planned. The Ult. Academy for Gifted Juveniles was built, as was an overseas academy that would eventually become the Future Foundation, and then there was the fourth academy: Hope's Pinnacle, for the D4 cast.
Before anyone gets to use Hope's Pinnacle as a school, however, Junko hijacks everything, and by the time the D4 cast reaches Hope's Pinnacle, it is now under Monochio/Monyochio's control.
(By the end of the saga, in the Hope route, the students reclaim Hope's Pinnacle and return it to the original headmaster, Esoran, also designed by Esora, but in her pre-Despair days. Esora's family helped fund and build the new academy since it was Esora's secret attempt at regining her Talent by enrolling in a new school).
The Tragedy:
While Makoto's class barricades itself inside of Hope's Peak, HA is on the move under the lead of Rinku, who is currently wanted for being an Ult. Hope. Because of her Talent (both as an Explorer and her unit's Ult. Hope), their travels take them around the country, combatting Despair.
Peaky's biggest role was in Twilight Syndrome Murder Case. Because of Yuka and Mahiru's matching Talents and ages, I headcanon that they became friends. Through Mahiru, Yuka also befriended Sato. (Esora was also part of this friend group, both because of Yuka, and because of Byakuya). Rei was another member just because of Esora even though Esora hid her lost Talent from everyone.
At one point, while investigating Sato's death, Yuka wears a red wig and calls herself Mahiru's cousin, Moeka Koizumi.
Photon, meanwhile, is far more spread out. While Ibuki unintentionally helps create and lead the Future Foundation, Noa struggles with her Nozomi alter ego, Towa is sent to Towa City to work on negotiations with the Towa Group, and Saki is left mostly alone back at Hope's Peak. Junko admits wanting Ibuki or Noa as Photo's Despair, but she settles for Saki because Saki is far more accessible to manipulate.
M4, under Rika's insistence, becomes a band of patrolling, ragtag heroes that frequent places such as Towa City. Dalia is a genuinely useful soldier while the other three unintentionally become parents to any Warriors of Hope or DICE members they meet. Saori uses her megaphone as a weapon like Komaru, Rika attributes her strength and combat skill to her volleyballing, and Marika is somewhat trained in combat thanks to Dalia and Mukuro. Marika knows Mukuro through Junko and she knows Junko because they have similar Talents. Marika even acts as Junko's "senpai" for a while before the Tragedy starts.
RONDO would've also been running back and forth between Hope's Peak, the Future Foundation, and Towa City, but mostly Towa City. Nagisa fights with her electric guitar and Aoi has mobile DJ turntables. And aside from the storyline with Kokichi and Kurumi, Miiko would've also been important during the Tragedy because her Horror Enthusiast Talent gives her meta knowledge and her gift with children means that working with the Warriors of Hope and DICE is marginally easier.
