Jenova is only hinted at but we can safely assume (s)he's part of an alien race who is actively at war with the Ancients. Aeris was the last Ancient alive on the Planet, so you can kind of see his motivation.
Jenova represented a perversion of the Earth, that's the theme of FFVII. Jenova is something like a perverse incarnation of the Earth's Spirit. It's actually partly taken from Greek Mythology. The Weapons (the large machine-like things that destroyed everything) are like the Titans, created by the Earth to defend itself against the Ancients, who represent the Greek Gods (post-Chronos of course). After the Ancients won the battle, humanity took the opportunity to discard their love of the Earth and eventually poison it until JENOVA was born. Like an infection, the Earth decides that humanity must perish. Sephiroth was created from JENOVA to become something like the anti-Christ (you can obviously see that from his final form). He does not offer salvation, only death. It takes the kind spirits of the dead to stop his power, showing that the Earth is wrong and humanity does have the strength to overcome its own shortcomings.
This is the general theme of all Final Fantasys. There are no aliens in even the most furturistic of Final Fantasies (not counting the Gameboy ones since they are actually part of Romancing Saga).
WARNING: Spoilers
Final Fantasy 1: Chaos, the incarnation of evil (reborn from Hell through Garland).
Final Fantasy 2: The Emporer, another incarnation of evil (reborn from Hell).
Final Fantasy 3: Dark Cloud, the evil energy from both Earth and Alternate Earth.
Final Fantasy 4: Zeomorus is the incarnation of one man's hatred.
Final Fantasy 5: E
eath merges with the Darkness to become yet another incarnation of evil.
Final Fantasy 6: Kefka enslaves the souls of the dead to become something like a god - a fallen god.
Final Fantasy 8: Ultimecia, a creature created from the Sorcoress being reborn from Hell.
Final Fantasy 9: Necron, another incarnation of evil (reborn from Hell through Kuja, this is a take-off of Final Fantasy 1).
Final Fantasy 10: Sin cleanses the Earth, this time Sin is more a part of the Earth and the Universe then truly evil. Sin more represents the Angel of Death.
So you see, all the Final Fantasys have a theme and a pattern.
1) Gather Heroes.
2) Enemy appears with maniacal plans to destroy humanity.
3) Enemy merges with either the Forces of Hell, or the Perverse Spirit of the Earth.
4) Heroes defeat the Enemy using the power from the good spirits of the dead.
The theme of Final Fantasy is usually an enemy born from hatred and/or reborn through Hell with an overall theme of Judiac-Christian with a mix of Shintoism, but every now and then the Shintoism overwhelms the Judiac-Christian theme as with Final Fantasy 7 and 10.
