Her ResponsibilityLead by Mitsuru's grandfather, Kouetsu Kirijo, the Kirijo Group funded and participated in numerous experiments with Shadows. Anti-Shadow weapons and equipment and evokers to call upon Persona were among the results of their experiments. They even used high school students as test subjects! Some people, a young Mitsuru included, were artificially given the "potential" to summon Persona. Kouetsu wished to harness the power of the Shadows and became obsessed with doing so despite the obvious dangers and shady ways of going about their research. Unfortunately, the researchers lose control of the Shadows and there is a huge explosion. The accident led to not only many casualties, but the existence of Tartarus and the Dark Hour. With their power and mass influence, the Kirijo Group covered the true causes of the accident and built Gekkoukan High School over the explosion site. Therefore, the Kirijo Group is completely responsible for all of those suffering from apathy syndrome, the attacks and deaths due to Shadows and for the creation of SEES in order to clean up their mess.
Mitsuru was only a small child at the time majority of this research was taking place. She had no real hand in anything that happened and was even used as a test subject for artificially creating the potential to use Persona. Even so, Mitsuru takes it upon herself to atone for what her family caused. She takes full responsibility for eliminating the Dark Hour and fighting the Shadows. Later on, she feels SEES and its members are also her responsibility. Why would a little girl take so much on her shoulders considering the danger? The answer is simple: her father. Mitsuru says that ever since the explosion, her father shouldered all of the responsibility and it looked like he was dead inside. She decided she would do whatever it took in order to reduce the shame and guilt he was experiencing, even if it meant sacrificing numerous things about herself. From the moment Mitsuru summons Penthesilea in order to protect her father from a Shadow, Mitsuru stopped being her true self. She shut off her heart and desires in order to have the willpower to take her family burden onto her own shoulders. Mitsuru wanted nothing more than to protect her father and take the burden from him. Therefore, there was almost nothing she wouldn't do in order to accomplish her goal.
Despite feeling guilty, Mitsuru explains how selfish she's been in both her social link with the female protagonist and in the drama CD New Moon. She only considered others in light of how they could benefit her goal. She aided in hospital experiments knowing they were wrong, forced friends into joining SEES to help eliminate Shadows while watching them suffer, get hurt and die. Mitsuru's true self did not like her choices, but she left that part of herself behind the moment she resolved to protect her father. In fact, Mitsuru left everything else behind. All she had was her responsibilities, resolve and ultimate goal.
It's not surprising, then, that Mitsuru loses her will to fight after her father's death. She no longer cares about Shadows, the Dark Hour or SEES. What was the point? Everything she fought for was in vain; her father is dead. The only reason she took on the responsibility of SEES and the Kirijo Group was for him. She felt chained to her family name, yes, but she threw away her true self and participated in things she normally would have been appalled by in order to protect him. But in the end, she failed. Everything was a waste. Everything was her fault because she was a failure. In the game, Mitsuru withdraws further into herself and does not partake in exploring Tartarus for a while. Further, in New Moon, Mitsuru actually gives her consent to SEES breaking up and no longer fighting the Shadows because they don't have a goal. She not only loses her reason for fighting, but her will to live. She put her all into protecting her father. Now that she didn't have her resolve, what would she do? She felt as if she had nothing to hold onto. Mitsuru even suggests that it might be better if she never wakes up again in the drama CD. There is no question about how important her father was to her. She discarded her feelings and desires, took on the weight of the world and acted in ways she hated in order to relieve him of any pain. Her sense of responsibility and dedication was to him, not to saving the world. When he was taken away from her, she felt she had nothing left.