Hypothetical situation post-Goblin's Gold at least. Basically, there's a creature in Camelot and both Morgana and the king want it out of the kingdom.
So Arthur, Merlin and Morgana go into the tunnels in search of it. That's not the point though. The point is the subject of the following conversation.
Merlin's question is one of those questions that should have been asked to Gaius at the end of Tears of Uther Pendragon Part 2.

Title of the fic is from Shakespeare's All's Well That Ends Well.

"Why am I not dead yet?" Merlin asked quietly. His words were amplified in the caves but Arthur was so far ahead that he couldn't hear what his servant had just asked. Merlin looked pointedly at the woman next to him. It was one of those rare cases where enemies had to work together whether they liked it or not. "Or more importantly," Merlin continued, "Why not Gaius? Or Arthur? Gwen?"

Morgana did not reply and just kept on walking, pretending that she was trying to find Arthur in the dim torchlight. "It would be the perfect time," Merlin pressed, trying to get a response no matter what it took. "We're in a maze of underground tunnels. We're looking for a magical creature. Why not just kill us now and get it over with? You'd have an alibi.

"Or you could have done it before. You could have killed me the first chance you got after I escape the serkets. Why didn't you? It would have saved you some trouble."

Morgana, still ignoring Merlin, continued to walk forward. "It's because deep down inside, and none of us know how small, there's a part of you that still cares," Merlin answered for her. Morgana froze, like a child caught stealing from the kitchens.

"What is it you want Merlin?" Her tone sounded just like Arthur's when he was aggravated with his servant. The only difference was that the sorceress's voice held more venom.

"I just want to know," Merlin answered gently and truthfully, "how a woman who was so sensible could suddenly be filled with so much hate."

"I don't need any pity," Morgana spat, starting to walk again, "and I especially do not need it from you."

Merlin caught up to her with the torch. "Then I don't offer it, but it doesn't make me any less curious."

"Don't delve into matters that you can't possibly understand."

"But I do," Merlin countered immediately. "And I know you don't believe it, but I do." Morgana laughed at his insistence. "I remember when you first told me about your magic. You were so scared, and you trusted your secret to me. I never turned you in and I never betrayed you."

"Then you poisoned me."

"Then you turned against Camelot."

"Against Uther."

"Against us," Merlin stressed. "Why did you never tell Gwen about your magic? Why did you just keep to yourself? Why did you trust us enough?"

"Because it's like Uther says," Morgana replied, voice choking with tears. "'To the heart of one sorcerer is to know them all.' To know the heart of one of Uther's subjects is to know them all."

"But that's not true," Merlin argued. "And you know that."

"Alright, you were the exception."

"And what about Gwen?" Merlin pressed. "Do you think she would've have told anyone? Magic saved her father once and for that she is grateful."

"It landed her in the dungeons and killed her father."

"And she accepts that, whereas you dwell on it."

"How many of our innocents have to be killed, Merlin, in order for magic to reign again?"

"How many innocent civilians who are able to decide for themselves whether or not Uther is right do you have to murder?"

"It's not murder; it's liberation. Anyone of them could be accused of magic. We've just saved them the trouble."

"Why not just wait? Wait until Arthur's king? People don't have to die. You could hide your secret until then. You could help people. The Morgana I knew would have done that."

"I'm still the same woman," Morgana defended. "And Arthur will be exactly like his father."

"Tell me you don't believe that."

"I do."

"He helped get the druid boy out of Camelot. He's saved my life before. He tried to sacrifice himself for me. Would Uther ever do that for a commoner?"

"I don't have time for your words Merlin. We both needed this creature out of Camelot. I suggest you walk faster." With that she quickened her pace and headed for Arthur's torchlight.

Merlin paused. After their long talk, Morgana still hadn't answered his question. "So why am I not dead yet?"