That is an idea I hadn't considered and would be very plausible. They boarded the Roosevelt and began assimilating the ship and crew, but were no where near ready before the Cube moved out of Wolf 359, or for the E-D's arrival. Then following the incident above Earth they were ordered to return to the DQ. They could have easily developed a transwarp coil and gotten out of UFP space before they were noticed. Thank you Guy.