See also: List of Blue Drop: Tenshitachi no Gikyoku episodes
Unlike both manga stories, the Blue Drop: Tenshitachi no Gikyoku anime series is set before the war. The storyline starts in 1999, with Mari Wakatake transferring to a girl's dormitory school called Kaihō Academy (海凰学園, Kaihō Gakuen?). Mari's background hides a traumatic past: four years before her arrival at Kaihō, all the inhabitants of the island where she lived died in one night. Mari was the only survivor, but lost all her memories prior that point.
At the academy Mari meets Hagino Senkōji, the school idol and class rep. Although Hagino is introduced as a calm and collected person, when she touches Mari's hand the viewer sees her freaking out and trying to strangle Mari. From then on, Mari is torn between anger and attraction towards Hagino, who pretends as if nothing had happened.
Unbeknown to Mari, Hagino is actually the commander of an alien battleship called Blue, which is the vanguard of the invasion to Earth. The incident on the island where Mari lived occurred when the crew of the ship and the island's inhabitants killed each other. Blue was seriously damaged and hidden, and Hagino blended into human society and continued her reconnaissance.
The story focuses on the relationship between Mari and Hagino; as Mari begins to come out of her shell, Hagino, who has been living a double life, gradually begins to have doubts about her mission. While the invasion and war draw closer unnoticed, they begin to understand each other