Blue Gender (1999)

At some point in his young life, Yuji Kaido has gained an untreatable disease and is cryogenically frozen until proper treatment is discovered. But when he wakes, Yuji finds that a mysterious race of Aliens known as Blue colonized Earth and almost extinguished the human race. Before he is attacked by them, a soldier in a mech named Marcelene rescues him to safety. Along the way, they have to adapt their plan so they can reach a new home: a place called Second Earth.