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Cain is a military leader who attained the status of a living war hero during the latter part of the Thousand Yahren War. Despite his popularity, Cain sometimes fails to live up to his reputation and seems quite unable to accept ideas other than his own. He is stubborn, but evidently knows how to run a military battlestar and execute a hindering plan against the Cylons.
Assigned to the Fifth Fleet as overall commander, Pegasus and that ill-fated fleet fought the Cylons at the Battle of Molecay. Presumed lost, the Commander managed to recover survivors from the disastrous battle and escaped to lightspeed. Since Cain knows that the Cylons would doubtless be between Molecay and the Colonies, he heads outward toward Gamoray.
Before the failure at Molecay and his presumed death, he apparently met Cassiopeia and knew Commander Adama. Both seemed to be friends of his, the former helping him recover from the death of his wife. As so far as is known, he has one daughter, Sheba, who matures into a Viper pilot that gave Apollo and Starbuck a run for their cubits prior to their discovery of Pegasus.
Cain oversees the continual "knocking down" of the Cylon forces on Gamoray, stealing fuel as the Cylons unwisely replenished and rebuilt. This is done with very little interference, since the Cylons are more intent on the Fleet assembled by Adama.
Sheba and Bojay encounter two Galactica pilots, who are subsequently brought before Cain for debriefing. While Cain mourns the news of the Cylon victory over the Colonials, and the utter holocaust conducted at the Colonies, he now has two battlestars at his disposal and nearly 200-240 fighting craft. This gives Cain an idea for taking over Gamoray and using it to strike back at the Cylons, which he presents to Adama, Colonel Tigh, Apollo, and Starbuck.
Commander Adama, senior officer to him, tells him that the plan is inadvisable and but will consider another alternative.
Sometime after presenting the plan to Adama, Cassiopeia visits Cain, who hears of his return through Starbuck. The two, while not being able to immediately warm up to him, went down to the Officer's Club. This caused Sheba, hating Cassiopeia for what she represented, to leave the Officer's Club.
Adama presents his plan on attacking the recently detected fuel tankers en route to Gamoray, using a squadron from both battlestars in the attack to raise morale. Cain, after some objection, goes along with the plan as well as conjoining the two major squadrons from the battlestars (Pegasus ' Silver Spar and Galactica's Blue). While Blue Squadron attacks the Cylon escort, Cain destroys the two tankers, hoping to force Adama into accepting his plan.
Adama isn't pleased, especially with Blue Squadron being deftly blamed for the destruction of the tankers. Cain presses on, but to no avail. Adama notes that Pegasus had a large enough fuel reserve to at least get the Fleet out of the system, but Cain disagrees. Adama has his fill of Cain's insubordinate actions and relieves him of duty.
Bojay and Sheba meet Cain in the Officer's Club of Galactica, informing him that they would help him regain command of Pegasus. He replies that he would do nothing that strikes as mutiny.
Cain later regains command of the battlestar Pegasus, admitting that if the two battlestars attacked Gamoray, there would be no Fleet left. As Pegasus is on the other side of the Fleet, he manages to sneak around and pin the attacking force of Cylon raiders, causing Baltar's forces to retreat.
Adama admits that the only way to now get fuel was from Gamoray, where the Imperious Leader would lead a dedication ceremony. Bojay, Sheba, Cassiopeia, Boomer, Apollo and Starbuck destroy the defense systems of the Cylon's outer capital, gaining access for fueling shuttles to take all the fuel they needed. Bojay is shuttled back to the nearby Pegasus, where Cain part ways with Sheba and Cassiopeia. Cain orders all unneeded personnel and Viper pilots off the ship via shuttle and Viper, while he, Apollo, and Starbuck attacked the two basestars. The basestars are positioned where they cannot fire without risk of striking one another. Cain, in a prime position, attacks both basestars after Apollo and Starbuck destroys the missile launchers of both craft.
Presumably, Cain and Pegasus are destroyed along with the second basestar. Yet, Starbuck incited speculation with the claim that Cain may have had Pegasus enter lightspeed before the base star's destruction.
Regardless, Cain's fate remains unknown to all those but himself and his crew (The Living Legend).