[@Lvl Down]Well, they are all the types of mavericks that X and Zero trash around the whole time in the games, so it's safe to say that friendly is a thing that they certainly aren't. By the way, it was the missile dudes that shot Commander D., they are bombing the other MH squads around the area, so disabling them is a priority. There's no viable way to attack the ship, other than deal with the maverick controlling it, who's waiting at the XZ monument.

After the highway there's a section inside the buildings before reaching the monument, by the way.