When he was a child, Murakami was friends with a girl he called Kuroneko. One day, while trying to prove the existence of aliens to Murakami, she is killed in an accident that he barely survives. Guilty of his role in the accident, Murokami decides to dedicate his life to proving that aliens exist. Then, one day, a new student with mysterious powers transfers into his class who not only looks a lot like Kuroneko, but is named Kuroha, Neko.
Murakami Ryota's best friend, Kuroneko, died in an accident trying to prove aliens existed when they were kids. Now, a girl who looks just like her transfers into his high school. When confronted Kuroha Neko insists she isn't Kuroneko, but she ends up revealing something else even more surprising...
Now that Murakami knows Kuroha is a lab-made witch on the run, he can't just leave her to fend for herself. Overcoming rejection, he manages to learn a bit more about her living situation... and her companion.
Murakami learns that witches need to take "death suppressants" in order to stay alive. Can they find a way to get more pills before tragedy strikes?
Having overcome the immediate death suppressant shortage issue, the witches start to settle into their lives as astronomy club members. A visit to the local onsen ends painfully for Murakami.
To welcome Kazumi and Kotori as members, the astronomy club goes stargazing on a mountaintop. Then Kana sees a forecast that wrecks the atmosphere.
The truth behind Kana's forecast of Kotori smiling over Neko's dead body is revealed, and Murakami has a possible lead on extending their pill supply.
The gang waits out the result of Kogoro's initial analysis of the pill to find out if he'll be able to copy it in time. Neko tries karaoke. Murakami and Kazumi head to Akihabara.
Murakami learns how reckless it is to act alone as he investigates the map. Meanwhile sex-obsessed Kazumi causes all kinds of awkward situations.
Lab witch Nanami and her handler are looking for #1107, but Ryota and the rest wonder whether they really have to be enemies. Couldn't they rescue her instead?
Kogoro is enlisted to attempt to remove the beacon from Nanami's harnest. Later on, Murakami motivates the girls to study for final exams by promising them a trip to the ocean.
Murakami's kindness is put to the test when a new witch shows up: is she friend or foe? Later, the truth about Kuroneko is finally revealed.
The identity of #1107 and the objectives of the witch lab are revealed as Murakami and the rest work not only to save themselves, but suddenly the whole planet.
Valkyria's relationships with both Ichijiku and Neko are revealed in the final episode. Will everyone make it out alive?
