Dr. Ayanokoji admires his creation - An Angel Heart Prototype Code Mark II named Kurumi. This experiment of his is the result of his efforts to save the world. Meanwhile, Nakahito is coerced into entering a mad doctor's mansion that supposedly has the detached living head of a dissected woman in the basement. The eleven-year-old Nakahito is drafted by his peers because he comes from a family of mystics, those who practice the Onmyou way. Dr. Ayanokoji, Kurumi and Nakahito are about to cross paths for the first time in a dramatic way.

Dr. Amagi attempts to coerce Dr. Ayanokoji into working with the Japanese military. When Amagi mistakenly grabs Nakahito, Kurumi rescues him. Nakahito and Dr. Ayanokoji discover they have another mutual associate. Kurumi displays jealousy when Nakahito hugs Kamahito. Dr. Ayanokoji and Kamahito misunderstand Nakahito’s explanation of Kurumi’s activation. Kurumi continues to question why she should proffer any significance to Dr. Ayanokoji. Dr. Amagi discovers another secret within the mansion.

A new character by the name of Dr. Brandow joins the Imperial Army, and even more interesting it seems as though he has been previously part of the Steel Angel Project. Meanwhile, Nakahito must now become accustom to rude awakenings,while Dr. Ayanokoji is convinced the Imperial Army will not be able to awaken the second Steel Angel prototype, but he is unaware of Dr. Brandow's contribution. All of this, of course, means nothing to Kurumi, who is agitated with boredom as Nakahito refuses to give her an order. When he finally does, however, it leads both himself and Kurumi to trouble.

The Imperial Army's preparation for the second Steel Angel's completion draws closer, during which Nakahito finds himself haunted by the words of Dr.Ayanakoji stating that only Nakahito has control over Kurumi. To make matters worse Nakahito is visited by some familiar characters,the end result leaving Nakahito even more confused and Kurumi afraid that her beloved master hates her. As though we thought things could not get much worse it seems the newly activated Saki is well on her way to causing trouble for Kurumi.

As Kurumi finds herself forced into battle with Saki, she hesitates, giving Saki the upper hand. In an effort to help, Nakahito seems to just make things worse and discovers that his words put Kurumi in this dilemma. As the fight continues it seems as though no one can help against the wrath of Saki. What will be the final outcome?

With the kidnapping of Dr. Ayanokoji it seems that in return a new (and unexpected) member has joined in his place. Saki quickly redeems herself as she helps to rebuild what she had at one point destroyed. It also appears that Dr. Brandow has disappeared with everything pertaining to the Steel Angel Project. Even more interesting is that Brandow doesn't seem to officially exist. This leads to the assumption that there may be an unknown party in all of this. Meanwhile, it appears that Nakahito, Kurumi, Saki, and their new partner are on their way to Izumo to discover the whereabouts of their missing comrade.

The group''s trip to Izumo comes to a halt when Nakahito gets a stomachache. So, Kurumi, Nakahito, and Amagi go see a doctor, but this doctor isn't your normal kind of doctor.

A large boulder is blocking the path of the train to our comrade’s destination. With two days of travel lost, Dr. Amagi searches for other transportation with little success. While the army tries to remove the boulder, Nakahito learns more about Dr. Ayanakoji's past from Dr. Amagi. As everyone grows impatient with the army's attempts to remove the boulder, Kurumi suggests that she and Saki remove the boulder. Dr. Amagi immediately rejects the idea at the risk of the villagers seeing them do what an entire army could not. However Kurumi and Saki have a plan of their own. Meanwhile it appears that yet another person is monitoring the Steel Angels.

The group spends a night at a fireworks festival, but the sparks really fly when Nakahito is kidnapped and Kurumi sets off to find him.

Kurumi finds herself fighting Nakahito's kidnappers, the Steel Angels Kaga, Tsunami, and Kaori.

A couple of incidents get Kurumi thinking that there is something going on between Nakahito and Saki.

Kurumi, Nakahito, and Dr. Amagi go to Kyoto to find Saki, who is beaten badly by another new Steel Angel, Karinka.

Kurumi fights Steel Angel Karinka. Can Kurumi's Mark II Angel Heart prevail over Karinka's two hearts?

Karinka disguises herself and tries to find out Kurumi's secret.

Karinka finds herself working as a waitress with Kurumi and Nakahito in an effort to find out the secret to Kurumi's power.

Karinka's new goal is to get a kiss from Nakahito so that she can become more powerful than Kurumi.

Kurumi and the gang finally arrives in Izumo, where they learn many secrets about Dr. Ayanokoji. Also, Nakahito meets a young boy...

Mikhail tells Nakahito about the potential danger of Kurumi's Angel Mark II Heart.

Kurumi, Saki, Karinka, and Dr. Amagi arrive at the Academy Base to rescue Nakahito. However, the Steel Angels fall into the Academy's traps, and Dr. Amagi meets face-to-face with Dr. Walski.

An angered Kurumi continues her search for Nakahito, but she runs into and fights Steel Angel Mikhail.

The battle between Kurumi and Mikhail continues. However, Kurumi is being consumed by demonic energy to the point that she grows black wings.

After beating Mikhail, the demonically possesed Kurumi attacks dr.Walski's base!

After Kurumi (in demon possesion) attacks the academy base, the damage is fatal. So in order to stop Kurumi, all the steel angels drain themselves to the point of de-activation to power the ultimate weapon to stop Kurumi's destructive powers.

Nakahito makes one final attempt to stop Kurumi from destroying everything.