During the mutiny I understood where Gaeta was coming from. Commander Adama was that nikka but you can't help but feel that Gaeta had a point with starting the mutiny against him.
Gaeta was accused of treason when really he was helping out the resistance during Baltar's administration ran by cylons.
His name was cleared but he's still shunned, and the circle that accused him ironically two of them turn out to be Cylons later on.
Later on he's sent on a mission with Starbuck who was supposed to be dead. He loses his leg when the crew fight over Starbuck forcing them to take a dangerous leap of faith on helping her find Earth. The guy who blows his leg off also turned out to be a Cylon later on
Then sure enough in an attempt to find Earth, Adama decides to team up with rebel Cylons forming a Human/Cylon alliance.
Gaeta gets mad at all the Cylons keeping their positions (he was taking orders from a Cylon XO lol), getting human benefits, he pretty much thinks Commander Adama lost his gotdamn mind. Where Gaeta fukked up though was getting Tom Zarek to help him out.