Gaia is the life force of the planet that gives creatures on the planet life. Every living creature has this spirit inside it, including humans. The researchers discover the 7th spirit is any phantom spirit that comes in contact with Gaia. Therefore, the phantom virus within Aki automatically becomes the final spirit since it is already in direct contact with her spirit, and the wave is complete. Gray sacrafices himself in order to transmit the completed wave into the alien life-stream, which eliminates the phantoms, and saves the world.
Continuity mistake: When Gray is being operated on by Aki (he's on the medical table) you can clearly see a reddish-brown scar on the lower left side of his neck (it's not a recent wound). It appears off and on for the rest of the film. Example: you can not see it when they are conversing after escaping to space in her ship after everyone else dies.
Trivia: Something to look for: somewhere in the film, the animators placed a Chocobo (one of those ostrich-like chicken things that people ride on in some of the Final Fantasy games). It's on the top right corner of Aki's shirt, almost the same color as the shirt, when she wakes up from her 2nd dream.
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