The two part finale opens with Merlin assisting Arthur in his chambers and poking a new hole in the king’s belt. It seems all the feasting has caused Arthur to put on a few pounds, and he makes Merlin promise not to tell anyone. Everything seems to be normal as they head off for another evening of celebration in the castle. Arthur turns a tad melancholic as he thinks of Gwen and shares a brief moment with Merlin.
But Agravaine has other plans for the evening, as he begins tossing small explosives at guards near the entrance to the siege tunnels and signals for Morgana and Helios’ army. He leads this advance unit through the underground passages. As they make their way through the town, they silently take out any guards they happen upon and spill oil throughout the market and around homes. Agravaine casually drops his torch to set ablaze his tracks. When Morgana sees the flames, she knows it is time for her to strike.
Leon and Elyan try to assist the people as much as they can in putting out the flames, but when Leon spots some of Helios’ men he knows there is more at stake than a few homes and shops. He sends Elyan to sound the alarm while he and a unit of men take on their attackers. Gawaine informs the king of the attack and Arthur has Merlin lead his guests to the inner chamber and orders the armoury sealed. Elyan runs into Agravaine with a handful of men in the halls and knows instantly that he is behind this. When Elyan moves to attack Agravaine, Morgana casts a force spell from behind her assistant, throwing Elyan to the floor.
Merlin and Gaius are doing what they can to aid some of the wounded. They have known all along that Agravaine was up to something and Merlin rushes off to find Arthur. While Merlin runs to search for his friend, Arthur and a few men are taking down those they have found inside the castle walls. Merlin finds Arthur just as he takes a blow to the stomach. With men on their tail, Merlin pushes Arthur to move on and pauses to distract their followers with some magic. From a hiding spot behind a pillar, the men watch in silence and Morgana and Helios lead their army to the citadel. He also sees his uncle join them, realizing his betrayal. Merlin urges him to leave now, telling Arthur they can worry about Agravaine later.
Leon is outside helping the people escape when he turns back and sees his home up in flames. He’s saved who he could and worries about his king.
Morgana sits upon the throne when Helios comes to bring her news of their triumph. He hasn’t captured Arthur yet, but he knows the king is inside the castle. Merlin has brought him back to Gaius for some medical aid, but Percival and Gawaine come back with bad news. Morgana’s men are only minutes from reaching them. Everyone knows Arthur won’t abandon his people but they are agreed that they must get him to safety. Gaius has nothing with him that could knock out his king and suggests to Merlin that perhaps he could do something. Merlin casts a spell that seems to make Arthur a bit of a puppet, doing whatever the magician says. Percival picks up Arthur and heads off with Merlin while Gawaine offers to stay behind to help give the men some time to escape. Gaius also remains behind, not wanting to slow them down. They stare Morgana in the face when she breaches the room hoping to find her half-brother, and when she realizes she is too late, Morgana calls for the horses.
Percival and Merlin have made it to the forest with Arthur and run into Elyan. As the foursome run and try to think of where they can find shelter, Merlin hears hooves coming up after them. Morgana and Agravaine are hot on their trail, with the witch using her magic in hopes of catching them. Elyan and Merlin scoop up Arthur, noticing a few seconds later that Percival is not with them. But they cannot stop to look for their friend. Once they’ve reached another trail, Elyan sends Merlin and Arthur ahead, staying back to give them some cover.
Merlin and Arthur seem to have run a fair distance and no longer have people behind them when Merlin realizes he needs to get Arthur some plainer clothing. Puppet Arthur is completely accepting of everything Merlin says. In the morning, they come across a small hut and find it abandoned but with some clothing that will help Arthur blend in. As he’s changing Puppet Arthur notes that the clothes are a bit too tight and even admits to Merlin that he should really think before he speaks, giving Merlin something to smile about. When Arthur comes out from changing, Merlin tells the king he looks like a turniphead and Puppet Arthur says nothing snarky back.
Agravaine reports to Morgana in the throne room that those knights who did not flee are either dead or locked in the dungeons. What she really wants to know is if the people have accepted her as their queen. When Agravaine informs her they refuse to swear allegiance to her, she tells him to have their crops burnt. Helios wants to know about Arthur, to which Helios’ men bring a captured Elyan forward. Morgana brings forth an Ethair, a small serpent she plans to use to torture Elyan for information on Arthur’s whereabouts. He of course refuses to give her anything, and his screams frighten even Agravaine. She emerges knowing where Arthur is headed, and warns Agravaine that should he fail again he’ll be in Elyan’s shoes.
Elyan’s broken body is dragged to the dungeons where he joins Gawaine and Gaius in a cell. Gaius sets to seeing what he can do for the poor knight. Morgana keeps them there without food or water for days before coming down to offer them anything. If they want to eat, Gawaine will need to fight for it. She brings him upstairs and pits him against the strongest of Helios’ men, offering him moldy scraps after each round won.
Though his men are ready to leave, Agravaine still has something he wants to say to an impatient Morgana. He warns her to remain cautious and not to fully trust Helios. Agravaine believes he is the best person to protect her, but she insists he is the only one she can trust to bring Arthur back to her. During their search, Agravaine comes by the shack where Arthur changed clothing, finding the king’s armour left behind.
During their trek, Merlin and Arthur happen to run into a band of smugglers also headed into Lot’s kingdom. When the leader is satisfied that these two intruders have seen nothing, he tells them they can go, but Merlin asks to travel with them. They buy passage with gold and are on their way. At night while they set up camp, Merlin stumbles on a load of frankincense and warns them that if they were caught they’d be in deep trouble. The man identifies them as Tristan and Isolde, and says they have nothing to fear of the half-wit king of Camelot (as Puppet Arthur hugs a tree nearby).
Around the campfire, Merlin talks to Puppet Arthur about his manners and how he treats Merlin. He sends Arthur off to clean the dishes and rub down the horses, all tasks Merlin usually takes care of. Merlin is finding this all kinds of amusing. However, things take a turn in the morning as Arthur is no longer under Merlin’s spell and curious to know why he’s dressed like a fool. Arthur is just a bit upset about being called a simpleton. Tristan notices Arthur carrying around a sword clearly crafted in Camelot and mentions that he’d be rather upset to find he’s been harbouring a knight of Camelot all this time. Arthur tries to play the part of simpleton to keep them safe in the meantime.
But as the exchange with Tristan ends, arrows start flying at the nearly disassembled camp. Agravaine’s men have found them and Arthur and Merlin offer to provide cover to Tristan and Isolde as it is their fault for this attack. They use crossbows to pick off a few of the enemy, then they head to hide with the other two nearby. They watch as Agravaine looks around for Arthur. Tristan realizes these men are after the simpleton and Arthur tells them who he really is. Their arguing is interrupted as men come up from behind them. Arthur stops Isolde from being killed and offers the smugglers to come with them to safety. They accept with Tristan making a point of saying he does this only for Isolde.
Arthur struggles to accept the fact that Agravaine betrayed him, despite Merlin’s warnings. He doesn’t understand why the people he loved have turned on him and Merlin believes it is the power Arthur holds is what they feared, wanting it for themselves. Merlin still believes in Arthur and reminds him that many others do as well.
When they arrive in Yldor, Merlin’s mother sees him and rushes to greet them. With a place to rest, Merlin treats Isolde’s wounds and Arthur apologizes to Tristan for the troubles he’s caused them. Merlin walks with his mother and the two catch up. They eventually stop at a small hut in the village where Gwen has been staying since her last run-in with Morgana. Gwen tends to Arthur as he’s resting, causing him to wake. He is shocked to see her and the two admit they’ve missed one another.
But these happy reunions are cut short when Agravaine attacks the village in the middle of the evening. Merlin causes a distraction while the others slip out around back, but Agravaine spots them and his men set chase.