A middle-school girl named Mikako Nagamine is drafted to the UN Space Army in a war against a group of aliens called the Tarsians, named after the Martian region (Tharsis) where they were first encountered. As a Special Agent, Mikako pilots a giant bipedal robot or mecha as part of a fighting squadron attached to the spacecraft carrier Lysithea.
When the Lysithea leaves Earth to search for the Tarsians with Mikako on board, Mikako's boyfriend Noboru Terao remains behind. The couple continues to communicate across interplanetary, and eventually interstellar space via the e-mail facilities on their mobile phones.
As the Lysithea travels deeper into space, the e-mails take increasingly longer to reach Noboru on Earth, and the time-lag of their correspondence eventually spans years.
The narrative begins in 2047. Mikako is apparently alone in a hauntingly empty city, trying to contact people through her cell phone. She finally says, in an empty classroom with stacked chairs, "Noboru? I'm going home, okay?", a rhetorical question which is answered with a busy line on her cell phone. Then she wakes up to discover that she is in her mecha orbiting an alien gas giant. She then goes to a moon or planet in the background, the fictional 4th world of Sirius System, Agartha.
In the middle of the anime proper, she sends an email to Noboru (which shows the date 2047-09-16), with the subject "I am here", saying "to the 24 year old Noboru, from the 15 year old Mikako" (in reference to time dilation, see below) which would only reach him 8 years, 224 days and 18 hours later, and just hopes it reaches him. Some flashes of imagery, perhaps indicative of memory, a hallucination, or even a mystical encounter, are then shown. It is a morphing character that looks like a younger Mikako. While they're speaking however, that character morphs into a Tarsian and then into an older version of herself. The same room where she woke up in the beginning of the animation is presented again, with the same ambience, but this time she is squatting in the corner, sobbing and pleading with her doppleganger to let her see Noboru just once more time to be able to say "I love you" to him.
The other being says "It will be all right. You will see him again". The ship's alarm starts warning her that the Tarsians suddenly coming from everywhere. Mikako cries even more, yelling "I don't understand!". A climactic battle ensues. Meanwhile, back on Earth, Noboru receives the message, albeit almost 9 years in the future. A voice-over dialogue commences between the two of them which functions as a synchronous soliloquy on the same subject. Meanwhile, back at Agartha, three of the four carriers equipped with the warp engines which brought the expeditionary force to Sirius have been destroyed. The Lysithea is still intact after Mikako joins the fight and stops its destruction. After winning the battle, Mikako lets her damaged mecha drift in space.