When the Cylons launched a surprise attack on the United Colonies of Kobol, the Colonial government ordered the immediate shutdown of the spacelines in order to keep civilian ships out of the battle. The Colonial Fleet, except for Galactica, was eradicated due to sabotage to their computer networks, leaving the civilian ships defenceless. Assuming the Presidency, Laura Roslin ordered all civilian ships to rendezvous at a designated location, including the Olympic Carrier. When Cylon Raiders discover the rendezvous point, all faster-than-light (FTL)-capable ships abandoned it for the gas giant Ragnar, where Commander William Adama of Galactica, having taken command of the remaining Colonial Fleet, was arming for a counterattack. Roslin persuaded Adama to abandon the Colonies and search for a new home, Earth.
Over the next five days, Cylon ships are able to track their location and jumped near the fleet's position every 33 minutes. It was eventually discovered that Olympic Carrier was unaccounted for after a fleet jump and presumed lost, but the loss also coincided with the failure of the Cylons to appear as expected, breaking the 33-minute cycle.
It later suddenly re-appeared near the fleet, and despite positive confirmation, Adama became suspicious and sent a Raptor and two Vipers to investigate. A voice over wireless communications explained that the ship had trouble with the FTL drive that took three hours to fix, and that the Cylons miraculously ignored them and left them alone.
When instructed to stay back, the Olympic Carrier broke orders and headed toward the fleet, and further instructions were met with silence. At the same time, the Cylons appeared, and when a radiological alarm indicated nuclear weapons on board Olympic Carrier, the Vipers were ordered to destroy it before it could reach the fleet.
Though not confirmed beyond visual inspection of an empty cabin, Olympic Carrier's complement were assumed captured by the Cylons, including Dr. Amarak, a Colonial defense researcher who urgently wanted to tell President Roslin about the presence of a traitor in the fleet.