Extraterrestrial mistakenly though to be a Cetra.
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Jenova is an alien lifeform that was mistakenly thought to be one of the ancient and dissapeared Cetra. The Jenova Project was headed up by a project headed up by Professor Gast and intended to produce more humans with the abilities of the Cetra, which Jenova, a world-devouring alien entity, was wrong thought to be a member of.
Approximately two thousand years before the main story of the game, Jenova arrived on the Planet via meteor travel. This created the Northern Crate, which the planet would hopefully channel Lifestream to in order to heal.
Jenova met the Cetra and infected many of them - which resulted in their such limited numbers. They do however eventually defeat the Calamity from the Skies and seals her/him/it up. Professor Gast later mistakes it to be a Cetra which results in Sephiroth's creation (birth). Sephiroth later learns of this birth and also incorrectly learns Jenova is a Cetra. He manages to steal Jenova's head, and later retrieves the rest from Shin-Ra after killing the President of the corporation.
In Final Fantasy VII, many of the most important characters including our Sephiroth, Cloud Strife, and Zack Fair have been injected with Jenova cells at some point in their lives.