Dr. Aki Ross
Infected with an alien herself, this scientists holds the key to defeating the aliens.

Gray Edwards

The leader of the elite Deep Eyes squadron, he is fiercely loyal and determined.  His biggest challenge may be his devotion to Aki (at odds with Hein's orders) 
Jane Proudfoot
A courageous, athletic, and proud member of the Deep Eyes squadron.  Because of her direct and foreceful nature, she often clashes with Neil.
Ryan Whittaker
Deep Eyes sergeants and second-in-command to Gray.  He is the model soldier, and recognizes Gray's leadership (who is also his best friend).  Ryan is determined and a 'fight until the death' soldier.
Neil Fleming
Neil is the intelligence agent of the Deep Eyes squadron.  Although he is sarcastic and pessimistic, he is also integral and reliable.
Dr. Sid
Aki's mentor, he is the genius behind the wave theory.  He guides Aki towards the final solution with fatherly and scientific advice.  The Earth's fate depends on his scientific visions.
General Hein
Taken with a hero complex and driven with vengence, he seeks to avenge the death of his family at the hands of the aliens.  Although he is a military strategist and skillful, his skill is overshadowed by his ego.  He will take whatever course necessary to destroy the aliens, even destroying the Earth itself.
Phantoms
AKA the 'aliens.'  They are brought to Earth by an impact.  Described as grossly asymmetric creatures, translucent, with enormous brains and tentacle arms, they are perhaps similar to the angels in Evangelion (?)

 

 

Meteor
Typical of the more recent Final Fantasy tradition, it crashes to Earth.  Not really a character, but one just can't leave such an integral part out.  It's impact brings the aliens to Earth (like the Second Impact, or the Lunar Cry perhaps?)

 

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