Dragonaut -The Resonance-

Two years after dragon eggs devastated Tokyo and killed people close to him, Jin Kamishina joins the military Dragonaut units formed to fight the alien dragons now nesting across Earth. His partner is Toa, an enigmatic girl bonded to one of the creatures, and together they're sent against dragons whose eggs keep destroying the ecosystems around them. Though it shares its title and cast with the Dragonaut: The Resonance anime, this manga tells its own version of the story, with different characterization and plot turns from the show.