This is the final battle with the Ultimate being which occurs after the final save spot on the aircraft carrier in the normal game. I basically conclude my first run through of the game and fight all the boss forms. With the current gun my character has equipped it allows me to use double commands which come in handy if I want to cure myself as well as attack. I refrained from adding any extra modifications to my weapons or armor to save these for the Ex game mode.
After the battles Aya blows up the aircraft carrier while the ultimate being is chasing after her. Once this is completed the ending and the credits roll. To clarify this is the standard ending you get by playing the game through the first time and not the second ending achieved by completing the Chrysler building in the EX mode.
For those who are wondering Aya’s current weapon MATT is just an engraved M9-3 found on the 3rd floor of the museum and her armor Ultimate is the engraved Cr Protector which is found in the Chinatown sewers.