Note: All 2.0 characters are now mostly the same age. They all kick off 2033 at either age 13 (first year) or age 14 (second year).
Prologue — 1.0 era: Circa 2013. A small army of students are encamped in the forest fending off wave after wave of terrible Island monsters. Many are forced to scatter, but a core group of rebelling students hold fast, break the attack on the forest camp, and begin to push toward the school to finish the battle once and for all. Several levels chronicle various minor battles across the academy, including the halls and Island, but the rebelling students are all eventually brought together in the courtyard for the final chapter. After defeating the Headmaster, made monstrous by his abuse of his powers and gifted genetics, a group of students enter the Headmaster's cellar, where they discover the comatose Diane and Phoebe Rivers. Scene fades.
Act I — 2.0 era: Circa 2033. The school is rebuilt and expanded, a stark contrast from the smoking ruins from the prologue. The children of the original veterans return to Beata Academy for the new school year. Over the course of the next few chapters, the player is led through daily Beata life, attending sparring classes, breaking up fights, getting dragged into a cafeteria brawl, going on missions abroad, etc. all while meeting various characters. Through small tidbits, they are fed the true backstory of the school through ghost stories and urban legends, all of which conflict on details, are exaggerated to comical extremes, or are straight up lies. There are various 'lighthearted' levels of this nature before there's a sudden and unexpected violent attack in the night, where a professor (controlling the school's defensive force field) is assassinated, along with attempts on another faculty which the player fights off.
This essentially kicks off the main story. The people in black, underneath their enigmatic leader under the alias 'Agrona,' turn out to be more than just another ridiculous urban legend as their activities ramp up across the world. Levels alternate between life at school and missions out in the wider world, which gradually begin to turn from fighting monsters to fighting people. During this, there's the occasional time skip and characters age and develop alongside each other, occasionally getting their own unique levels which shape their own motivations in the growing shadow war between Beata and Agrona's legionaries.
Throughout this time, different characters receive subtle hints of information of what's happening outside Beata, including the fall of Sofia Academy under Agrona's influence and her growing numbers. A large-scale level where a conspiracy to destroy a major city is thwarted by Beata students is the tipping point. This culminates in a threat that's issued to the school, telling them to bend to her will or be destroyed. A large army of people in black begin to march, with several smaller battles leading up to the final climactic chapters of the act, in the battles across the academy grounds. Beata once again is reduced to smoking brick ruins, but the school prevails and the attacking forces are routed. Graduation is held in the shell of the Great Hall in a scene that mirrors the introduction to the act.
Act II — 2.0 era: Circa 2039. Beata has no choice but to push forward on an offensive campaign to have any chance. While outnumbered and outgunned, the students blaze a trail across North America and Europe as they push toward Agrona's new head fortress of Sofia Academy. This is more chaotic and action-packed than the previous act, with battle after bloody battle. Eventually, despite all odds, they reach Sofia, where the biggest fight of the game so far breaks out. By the end, Agrona's main forces are all dead or scattered, with all her officers defeated. They push on deeper into the school itself where they find her and prepare for the final struggle of the war.
Plot twist. Everyone dies.
Agrona is so horribly OP, that unlike the fight against her father in the prologue, about everyone is OHKO'd the moment they come within range. You probably won't even be able to dent her because she's got mad HP. Surviving an initial attack leaves the unit incapacitated and writhing in madness, where she'll likely finish you off in the next turn.
The point is that you all die. Actually die. For real. Forever. It's brutal.
Act III — 3.0 era: Circa 2054. Beata still stands thanks to the sacrifices of the previous generation, but it's a changed institution. The orphans of the war have grown up closer than family, slumming it out under the walls of the citadel that Beata has transformed into. All in all, these are more violent times. Children are involved in bitter fights for survival by the time they're old enough to attend Beata, and the gifted world is drawn in two, between the black-suited revolutionaries that now dominate most of the globe and Beata's small empire that continues to expand across the continent. Characters fight alongside each other and grow to forge deeper bonds, as they struggle against a world increasingly overrun with monsters loosed by erratic portal behavior and the seemingly never-ending war between two powers bent on the total annihilation of the other.
Throughout the act, the people in black are portrayed as increasingly sympathetic as Beata grows crueler in its desperate search to find an edge. Finally, it is revealed that Beata is using equipment left behind from the original Headmaster in the prologue to prepare a supernatural weapon, which will destroy the Island dimension and harness that sheer explosive power to use in the war, but at the cost of widespread destruction on a global scale. Hidden consequences are hinted at, but nothing conclusive is explained. The orphans are firmly split over what to do and turn against each other. Half join Agrona's forces, while the rest continue to stand with Beata. From this point on in the act, levels alternate between the two groups, and characters begin dropping off like flies left and right. A subplot follows a group of defectors who are determined to destroy the weapon at any cost, and work against the clock as it grows closer to completion. The war flares up to an unforeseen intensity.
The final chapters alternate. A final climactic battle breaks outside of Beata, where Agrona is leading the charge herself. Meanwhile, the defectors infiltrate the academy to disable the weapon. The defectors find the weapon within the portal itself, which is revealed to be a strange ancient machine banded with light that stands heavily guarded. The Beata students guarding the weapon are killed, but the moment the people in black reach out to touch it to try and prevent it from firing, it explodes in a burst of radiance that vaporizes the surrounding radius. The sky tears, bleeding black, and the Island dimension is destroyed in a violent rip that resembles the fabric of reality itself being pulled into a vacuum.
Outside, explosions tear across the sky. Hurricane force winds, earthquakes, and tsunami-like waves are reported from all across the world. The Island monsters in Agrona's army are turned to ash where they stand. Beata, with genetic material preserved from the prologue, had engineered a weapon designed to rend apart her gifted genes. Agrona's capillaries burst. Gifts across the battlefield flare into godlike earth-shattering power as the gifted themselves begin to change. Almost everyone is killed in the ensuing clash.
Torrential rain pours down as the level finishes. Everyone is lying in a desolated landscape. The surge of power fried the synapses of anyone who survived the initial battle. One final character is left, who raises their hand to realize their power is now gone—permanently.
Beata has won. Headmaster Lupo walks through the rubble of Beata Academy and howls to the moon, fist pumping. Freeze frame. Credits.
https://www.youtube.com/watch?v=0jlHz0wF0Ig 
