In The Time Of Magic
Merlin told Morgana about his magic, and they've been saving the innocent sorcerers since the beginning, but Morgause enchanted Morgana to do her bidding. During the 3rd season Morgana's trying to break away from Morgause, but during the season finale everyone believes that she's actually turned evil, so she leaves with Morgause. The only way to break the enchantment is to sacrifice Morgause at the Veil, and Morgana's very sorry that Lancelot ends up dying, but Merlin forgives her.
She believes that Uther is the cause of all evil in Camelot so she plans with Agravaine, who is good but her spy, to let him die when they learn about a plot to assassinate him.
During the stuff with Caerleon the rest of the knights and advisors believes that Arthur should execute him, and Arthur can't quite disagree with them openly, but he complains about it to Merlin, so Merlin secretly releases Caerleon and confounds him to think that he saw the knights of Camelot defeat his best fighters so he decided to back off from attacking Camelot.
Morgana has the magical coin which she uses to bring back Lancelot, but seeing that he's not quite right she, Merlin and Agravaine go on a trip to the Cauldon of Arianrhod to get back his soul.
Everything ends happily.