Nagisa was born and raised in Towa City. He was a child prodigy and raised to be a perfect child and one of the society's elites. His father was a teacher at Hope's Peak Academy's Elementary School division which Nagisa attended and as a result, he expected his son to be the best. He was in the class of troublemakers along with Monaca, Jataro Kemuri, Kotoko Utsugi and Masaru Daimon, though he resented being labeled as a "troublemaker". Supposedly, he developed a crush on Monaca at this point, due to her seemingly kind nature.
Nagisa's parents' mindset on raising him is similar to playing a game. In order for Nagisa to "gain EXP and level up", he had to study for unhealthy lengths of time. He would be connected to an IV with energy supplements to "restore HP" when it looked as if he would pass out from exhaustion. He was also constantly observed with cameras.
Nagisa's father forced his son to study non-stop for days. He would do things such as shine bright lights into his son's eyes if he looked as if he were becoming tired at any time other than the short periods he was permitted to sleep. He was also threatened with weapons and other physical abuse. In one of the in-game CG, a knife can be seen on the corner of Nagisa's desk as well as several drops of blood, implying its use. Nagisa's participation in all of this was in the name of an experiment that would try to determine just how much mental and physical stress a child could take before reaching their breaking point.
As Nagisa's father didn't get the experiment results he was hoping for, he didn't see wrong in his way of doing things and instead started to consider his son a failure as a test subject. It's also implied that the parents were considering having another child and restarting the experiment with a fresh test subject.
When Nagisa found out that he was falling short of his father's expectations, he felt such strong self-loathing and guilt that he wanted to die. He felt that he hadn't done anything right, even when there were such high hopes for him. He questioned why he was the way he was, why he wasn't born better and why he wasn't the child his father wanted. Because "only hopeless idiots fritter away their lives with self-hatred", Nagisa decided to just ignore the pain he felt and worked even harder and harder, no matter how high the expectations would be. He didn't want to disappoint his father ever again.
Although Nagisa was on the verge of committing suicide along with the other Warriors, Junko Enoshima appeared and convinced the children that the adults were wrong and that they should create a paradise for children. Nagisa murdered his parents shortly after, expressing some guilt afterwards.
