He had promised Remy he'd stay safe during this and not end up like the other version of him and Pepper. He'd been in his armor and still ended up dead, so in this case, the only thing he could do was use it to dodge her and attack from the air.
"Will this make her vulnerable to particle beam attacks? I can stay in the air, move around and hit her fast. KITT, I'll patch you into my HUD so you and Bobby can keep in contact with me while I'm up if you need me." Once he got his answer from them, Tony would slide his helmet back into place and take off.