Arthur, Gwen, Tristan, Isolde and Merlin have reached the woods just outside the village, but Agravaine is hot on their tail. Merlin urges the others to keep going, offering to cover their tracks. With the others further ahead, Merlin calls his friend the Great Dragon to aid him. While Merlin runs to meet up with his friends, the Dragon comes up from behind and attacks Agravaine’s men. When the Dragon comes around for a second pass, Agravaine and his remaining companions flee in the same direction Arthur’s party has gone.
Merlin aids his friends through the tunnels he used to play in as a child, a little fuzzy with his memory as to which way they should go. As they crawl through narrow passages, Tristan asks Gwen about herself and why she follows Arthur. The noise the group makes as they continue on has alerted Agravaine to their whereabouts. Merlin again offers to go back and create a diversion, and after Arthur tells him not to do anything stupid (he can’t just simply say “Be careful”, can he?), Merlin backtracks to a larger corridor.
Merlin leads Agravaine in another direction for a bit, letting him catch up. Agravaine threatens to kill Merlin if he doesn’t tell him where he is, but Merlin shrugs it off. As Agravaine takes a step towards him, Merlin uses his magic and throws the men back against the cavern wall. Unfortunately, Agravaine isn’t down long and realizes that Merlin is Emrys, complementing him on getting so close to Arthur. But when Merlin ignores a gesture of friendship, Agravaine draws his sword. Merlin counters by blowing him back harder so that the traitor’s skull cracks against the rock, finally killing Agravaine. Once Merlin is sure the king’s uncle cannot follow him, he turns to catch up with his friends.
Arthur has the party stop when he hears footsteps coming closer to them. He runs off only to find Merlin, admitting he came back to find his only friend, but making light of it by acting as though it was a joke.
When they come out on the other side of the tunnels, the group needs to decide where to go. They can’t venture into Lot’s kingdom as he is no friend of the Pendragons, and as fugitives of Camelot they’d risk the lives of anyone who gave them shelter. They end up heading toward one of the greater forests surrounding Arthur’s castle, hoping to find others who’ve survived Morgana’s army.
Meanwhile, back in the castle, Gawaine and Elyan tend to Gaius as best they can inside their cell. Gawaine is dragged off to fight for their supper with Morgana giving him a wooden child’s sword as his only weapon. If he wants to help his fellow captives, Gawaine must defeat a couple dozen of Helios’ armed men. He’s brought back successful once more with Morgana tossing the men a moldy chunk of bread and warning them that it will be their last meal. Elyan tries to get Gaius to eat, but the physician knows he doesn’t have much longer to live.
Tristan still hasn’t figured out Arthur, confused as to why the king would go back to rescue a servant and then help out by gathering firewood instead of leaving it to the others. He reminds Arthur that he really is just like everyone else now, no longer king as his throne has been taken away. Tristan walks back toward Isolde, giving Gwen a chance to talk with Arthur. Arthur insists that everything there was between himself and Gwen is gone now, and all she can do is apologize once more.
The former king of Camelot stares into the campfire contemplating recent events. He’s beginning to lose faith in himself, blaming himself for believing in the wrong people. Merlin tries to remind Arthur that he is a great king and leader, but Arthur is too busy having a pity party of one. Unsure of what he can do for his friend, Merlin calls for the Dragon to meet him in the woods. He tells Merlin that only he can convince Arthur that he can be a king again and that there isn’t anything he can do about it. Standing there, a plan begins to brew in Merlin’s head and he asks the Dragon if he can help him find the survivors.
In the morning, Merlin wakes up Arthur and leads him through the woods. He wants to tell Arthur a story he claims Gaius once recounted to him of a sword that the first king of Camelot plunged into a stone to be a test should there be a question of one’s validity as king of the realm. Merlin leads Arthur to the very rock he stuck Excalibur into, and upon seeing it, Arthur believes that Merlin’s tale may indeed be true after all.
Arthur walks toward the sword in the stone, and as he does so, survivors walk out before his eyes to bare witness. Among them are Percival and Leon. Arthur has a feeling that Merlin is up to something, especially because he views the task of pulling a sword out of a rock as impossible. With his hands wrapped around the hilt, Arthur makes a first try to removing the sword. Merlin stands behind him, urging his friend to believe in himself and have faith. Arthur tries again, with a single hand gripping it in a familiar stance, closing his eyes and before everyone gathered, drawing the sword out and high into the sky above him.
Helios brings Morgana some rather disheartening news. His men found Agravaine’s detachment burnt and Agravaine himself dead. Morgana is sure that this was Emrys and walks away from her accomplice frightened.
Arthur and his men makes plans to infiltrate the citadel and reclaim Arthur’s throne. Leon and Percival insist that the men fight not for Camelot, but for Arthur – an exchange that Tristan and Isolde witness. It appears as though the two have a changed opinion about the man they once hated. Arthur tells Merlin he isn’t worried about Helios’ men, but Morgana. His half-sister has grown so powerful and he has nothing that can match it. Merlin then tells Arthur there is one last piece to the story he was telling earlier. That the man who would remove the sword from the stone would become the greatest king Albion would ever know.
While the others get some rest, Merlin breaks into the castle and transforms himself into his Emrys form. He wants to scare Morgana and makes sure she catches a glimpse of him in the halls. After losing some guards, Merlin heads for Morgana’s chambers and places a hex under her bed. Then he steals a guard’s uniform and slips away. Helios escorts Morgana to her room where she tries to get some rest.
Arthur’s army prepares to set off for the citadel, and when Tristan and Isolde approach he is ready to say goodbye to them. However, after seeing how Arthur truly acts and treats his people, the pair offer to fight at his side and he accepts them warmly. Gwen also approaches Arthur and tells him that she understands why he can’t forgive her; she only wants him to know that she never once stopped loving him. She then walks away before he can say anything in response.
Armed with all they could find, Arthur’s army moves on the city. Split into smaller groups, they take out as many sentries as they can before the alarm bells are rung. Arthur fights his way toward Morgana while the other groups do as much damage as possible. Percival and Leon head to the dungeons to rescue Gaius and the other prisoners. The clanging of swords rings throughout of hall of the citadel and Morgana knows Arthur is nearby.
Ready to storm the throne room, Arthur knocks down the door and expects an army around his sister. Once inside, his group is shocked to find only Morgana and Helios present. Arthur is sad to see Morgana as she is now and tells her she can’t blame him for Uther’s actions. The two acknowledge that they are both like their father to some degree, and then Morgana moves to attack her brother. However, her spells will not work and she flees the room with Merlin and Gwen chasing after her. Arthur, Tristan and Isolde remain behind to take care of Helios and his approaching men.
Arthur and Helios are going at each other when Helios manages to land an elbow to Arthur’s jaw, causing the king to stumble. As he readies his sword to plunge into Arthur, Helios is run through by Isolde. But she doesn’t get away clean as Helios manages to swing his sword around to run through her stomach.
It is Gwen who finds Morgana in one of the hallways, the witch with a fresh abdominal wound. While they exchange blows, Gwen asks what she’s done that’s made Morgana hate her so much. Morgana replies that it’s nothing she’s done but what she’s destined to do as she disarms her old friend. With Gwen staring down Morgana’s blade, Merlin hides behind her and uses magic to push Morgana back and cause part of the ceiling to crumble over her but when he looks to where she was, Merlin sees her missing. Merlin and Gwen rejoin the others in the throne room where Tristan holds his dying Isolde. Arthur and Gwen look at each other with tears in their eyes across the room.
A day or two later, Gwen is cleaning up one of the rooms in the castle when Arthur finds her and admits he doesn’t want her to leave. He asks her if she will marry him and she quickly agrees. They are promptly married and Gwen crowned Queen of Camelot.
Morgana has been stumbling about powerless and wounded for days, when she finally falls over and dies. Only she’s not dead for long as a grown up Aithusa breathes life back into her before flying away.