okay but scarlet nexus lore
i'll have to explain the base lore first might take a bit
so somewhere in futuristic japan, people discovered a hormone in the human brain which evolved into powers. these people with powers became known as Psionics. Around the same time, a veil of Other Particles (eventually becoming known as the Extinction Belt) covered the earth, just above the stratosphere. grotesque brain eating creatures known as Others descended from the Belt. the thing is, they were weak to powers, and immune to basically everything else, so the Psionics formed the OSF--Other Supression Force. Since then, the OSF have developed a bunch more cool stuff, like SAS (Struggle Arms System), which allowed Psionics to temporarily borrow each other's powers, BIAS (like i said, the reddit assumes its called Brain Integrity Augmented System), and Brain Drive, as well as a (very powerful, but equally dangerous) extension, Brain Field.
now for the actual explaination
Kasane's platoon (Kasane, Naomi, Gemma, Shiden and Kyoka) and Yuito's platoon (Yuito, Nagi, Hanabi, Tsugumi and Kagero) were tasked to clear out an abandoned line of Others. Naomi (who is the girl Nagi has a crush on) gets shot with a bullet containing Other Particles, to save her sister, Kasane. She gets turned into an Other. (process called Metamorphose)
Nagi, seeing this along with Yuito, Kasane, Tsugumi and Gemma, becomes traumatized, so he gets sent to the OSF hospital for therapy. Instead, he gets put through Personality Rehabilitation, which is as bad as it sounds, if not worse.
(he ends up killing his platoon leader, Seto, while under PR, in an event shortly after Naomi's Metamorphose.)
The New Himuka government forces BIAS, Brain Drive and Field on Nagi, even though his mind isn't compatible with any of them. So the combined stress of those, plus him trying to resist PR, ends up killing him.
Naomi dies as an Other, while saving Kasane, Shiden, Kagero and Luka (luka is another character). Naomi dies in peace, knowing she did all she could, while Nagi dies with a shit ton of regrets, not only trying to kill his best friend, but killing his platoon leader, and not knowing what happened to his crush (naomi) in the end