In the year 2035, the attempt to create an Artificial and Intelligent Cellular Organism went horribly, horribly wrong, causing the Burst, which covered Kurobe Gorge in synthetic organisms called Matter. The area became uninhabitable, and a small industry sprang up of mercenary Divers who venture into the gorge and fight the Matter in order to recover valuable items for rich clients.
Two years after the Burst, teenager Aiko Tachibana has almost completely recovered from a car accident that killed her father and left her wheelchair-bound. On the last day before summer vacation, a new student, Yuya Kanzaki, transfers to her school. Yuya reveals to Aiko that her body is artificial and that the her real body is stuck somewhere in Primary Point, the area where the Burst began. He also informs her that if she goes to Primary Point, she can help end the Burst once and for all. Enlisting a team of Divers, Aiko and Yuya head into the gorge.
This series contains examples of:
- Ambiguously Human: Aiko's body is made of artificial cells, making it both resilient to harm and a beacon for the Malignant Matter. Aiko is the first and only known case of an artificial organism with an artificial brain. Both she and the rest of the team wrestle with whether that makes her a human or something else.
- An Arm and a Leg: Kazuki lost his right arm in a Matter attack, and had it replaced with a prosthetic. Over the course of the series, he has to replace the arm a few times.
- Clingy Costume: The suits that the Divers wear are made of artificial organisms, and attach to the body like a second skin. After Aiko puts one on, she has trouble getting it off again.
- Color-Coded for Your Convenience: Every member of the exploration team has a suit of a specific color.
- Likewise, the matter that's under Aiko's control is colored red while the matter controlled by Yuzuha/Dr. Isazu is purple.
- Clones Are People, Too: The artificial Aiko at the end of the series.
- Disappeared Dad: Aiko's father died in a car accident.
- The Dulcinea Effect: Kazuki is quick to fall for Aiko and even help during her initial escape attempt from the group without even knowing what was going on.
- Her Heart Will Go On: After Daisuke's death, Shiraishi struggles with grief, but ultimately pulls through.
- It's All My Fault: Aiko blames herself for pretty much anything that goes wrong during the journey, frequently exhorting her comrades to turn back so that they won't suffer further on her behalf.
- Meat Moss: The Malignant Matter, a hostile organism that has swallowed Kurobe Gorge in rapidly-growing flesh. The series loves this trope.
- Mentor Occupational Hazard: Shino is looked up to by all the other divers and is the only member of the group to die during the mission.
- Ridiculously Cute Critter: Gummi, the hamster made of artificial cells, serves as the Team Pet and Familiar to Aiko.
- Shout-Out: In an otherwise pretty serious and self-important anime, Project AICO being mispronounced as Project A-ko by a character almost seems somewhat jarring.
- Team Mom: Maho Shirashi provides much of the team's tactical and emotional support.
- Tomato in the Mirror: The Aiko that the series follows is actually the brain of the artificial Aiko (or "A.I.C.O.") in the real Aiko's body, while the Burst is the result of the artificial body reacting adversely to the real Aiko's brain.
- "Where Are They Now?" Epilogue: We get one of the main cast at the end of Episode 12:
- The original Aiko returns to having a normal life at school and home with her mother and brother.
- Yuzuha returns to having a normal life in recovery, whilst her father is still stuck in a comatose state.
- Kurose regains his position and goes back to work at the research lab with Haruka joining him.
- Kazuki is working at centre for those with prosthetic limbs.
- Kaede is working as a kindergarten teacher.
- Yoshihiko is a rescue worker.
- Nanbara and Hori return to their old job positions, performing a presentation on the now cleared area beyond the gates.
- Shiraishi visits the site of Shino's death and leaves a bouquet whilst watching the reconstruction effort for the area.
- And finally, the artificial Aiko transfers into a brand new school to start a new life and create her own memories.