In the seventh episode of the third season of
Battlestar Galactica, "Hero," we learn that before the first Cylon attack at the beginning of the series, Adama was involved in something illegal that he's been hiding all this time.
The two-part tenth and eleventh episodes "Eye of Jupiter" and "Rapture" find the crew landing on an empty planet called Algae and presumably capturing a prisoner there; in the following episode ("Taking a Break") the crew thinks their new prisoner may well be a Cylon – and so does the prisoner. This episode is directed by Edward James Olmos.
In "The Woman King," an episode that may be the thirteenth of the season, many of the people of the fleet are sick and dying. The mother of one of the deceased, a Sagitarron, believes her people are not receiving the same medical treatment as others among the colonists. Helo investigates a Doctor named Robert (or Roberts) against whom there have been a lot of complaints. Then first Helo's own daughter Hera (the half-Cylon) and then his friend Hot Dog become patients of Roberts.