In the Ending the Protagonist dies.
When the computer, the final boss, was defeated, it caused an explosion that the protagonist was unable to block from. Thus, it led them to there death. The character that the Protagonist sees in the end is their Gunbike in soul form.
Why the character's Gunbike would have a soul at all might be because the character had such a strong connection to their Gunbikes that a soul was formed from the Gunbike's AI.The villainess boss that appears at the end is Major Nouno's sister