Mitsuki knows that she’s built differently than anyone else. That she thinks differently. Is different. Mitsuki sees the world in patterns and codes. Her intelligence and her gift of cryptography brought her to the attention of the Japanese government at a young age. With such intelligence, Mitsuki has struggled with emotions, the social elements of life, but has been able to “pass” as human. But Mitsuki feels distant from most human beings, until she meets her lover, Hinata. When Hinata is killed at the start of the series, Mitsuki stops at nothing to seek revenge against whatever killed her one true love, but that journey takes surprising turns.
Saying goodbye to Hinata
Mitsuki is in a secret relationship with Hinata when she is scheduled to go on a year-long trip to the International Space Station. However, Mitsuki is fortunate enough to get a chance to say goodbye when she is instructed to check the backup comms inside the shuttle. After repairing the comms and whispering something to Hinata, Mitsuki watches from her station as the shuttle takes off.
Mitsuki rushes back to work after learning that they've lost communication with the shuttle, which they eventually discover has ruptured and that the astronauts on board, including Hinata, are believed to be dead. So, Mitsuki forces herself to move on with her life now that Hinata is gone, though that proves more difficult than she initially thought, unable to even have sex with another woman without the thought of Hinata crossing her mind.
Mitsuki struggles to cope with Hinata's death, though she forces her way back to work anyways. And when she discovers that they've been taken over by an independent commission, Mitsuki steals Hashimoto's badge and breaks into the comms room with Kaito. Together, they watch the final moments of the shuttle before it ruptured, discovering that something hit the shuttle. And when Mitsuki enhances the audio, she hears the word "Wajo."
Meeting Hinata's father
Mitsuki insists that something hit the shuttle, which caused it to rupture, but after being fired from JASA for breaking into the comms room, she decides to pay Ikuro Murai, Hinata's estranged father, a visit, and play him the audio from the shuttle comms of Hinata’s final moments.
Investigating the shuttle rupture
Mitsuki returns to JASA after being fired and plays Hashimoto the enhanced audio from the Hoshi-12 before it ruptured. The phrase "Wajo" can be heard, suggesting that the shuttle didn’t depressurize and that there could still be someone alive up there. From Hashimoto, Mitsuki learns that they now know the shuttle made contact with extraterrestrial life. With his blessing, Mitsuki steals some equipment to do her own independent investigation.
With help from Kaito and Ikuro, Mitsuki infiltrates the satellite station as an authorized JASA official in an attempt to hopefully make contact with the aliens using the audio from the last moments of the shuttle, which they’ve turned into a spectral fingerprint in hopes of finding whatever is broadcasting it. However, Mitsuki realizes that they aren’t searching for a broadcast at all, rather a network and then spots an anomaly, which they discover is the distress beacon from the shuttle.
Mitsuki is taken into custody yet ultimately manages to bargain for her freedom as well as lead the comms team. Mitsuki transmits thousands of files, videos and images of Hinata, to the aliens as a form of visual format that the aliens can comprehend. Suddenly, they hear back. "Wajo" is repeated over all frequencies.
Making contact with Hinata
Mitsuki makes contact with whom she believes to be Hinata, restoring all hope that she may one day be reunited with her lost love. However, not only is Mitsuki being used as a distraction until the U.S. military can nuke the aliens, but according to them, the voice Mitsuki is hearing is synthesized, suggesting that Hinata is in fact dead.
Mitsuki is forced to mourn Hinata's death once more following the U.S. military's nuclear attack, which seemingly stopped the invasion. She first heads to Hinata's home before hitting the road, where she encounters an odd weed-smoking Monk, who offers her shelter at the temple. There, Mitsuki hacks into the satellite station and attempts to make contact once more.