A scout ship was used to retrieve Rex after his battle with the Multi-faced EVO Agent Six later used a scout ship to rescue Rex from Abysus, but although Six survived the attack by Van Kleiss, the rest of the Providence agents and a few scout ships did not.
Another scout ship was used in order to transport Rex, Bobo, Dr. Holiday, and Six to Paradise base after Rex suffered a nanite overload. When the group were forced to evacuate the facility, Rebecca and Bobo grabbed control of the scout ship before nearly colliding with Paradise.
Underneath the scout ship is fastened a large metal box-like container complete with Providence signature, pulled by strong metal cables, presumably for capturing or escorting large EVOs. It also can be used to secure other heavy cargo, such as Caesar Salazar's pod laboratory. The container can be ejected and used as a temporary research camp.