Manga: Biomega.

Biomega is an Surrealistic Cyberpunk action manga by Tsutomu Nihei. It follows a character by the name of Kanoe Zouichi-a synthetic elite soldier created by Toha Heavy Industries and his AI companion Kanoe Fuyu whose luminous form is integrated into the system of his 4000XLA Toha Industries Motorcycle.

The 4000XLA Toha Industries Motorcycle

Fuyu assists Zouichi with situational analysis as well as advising him on strategies. Like the other AI's in the comic series she has had emotions programmed into her. The bike itself comes equipped with a rifle, a hand held railgun, and an axe for close combat.

Biomega is the second prequel to Tsutomu Nihei's highly successful Blame! series. You can download translated issues of Biomega here.