A year after being whisked away from Camelot, Morgana is found, disheveled and bruised in the forest and claiming abduction by bandits. Superficially contrite and charming, she remains in league with Morgause, for whom she collects tears shed by Uther. These Morguase uses to curse him through a doll fashioned from mandrake root, which Morgana places under his bed. As it slowly starts to drive the king mad with hallucinates of ghosts, Morgause - after taking Merlin prisoner - induces rival king Cenred to invade the weakened kingdom, for which Merlin summons the Great Dragon for aid.

The Great Dragon returns Merlin to Camelot where, convincing Gaius of Morgana's treachery, they break the curse on Uther by burning the mandrake doll. Nonetheless, they feel he would not believe them if they exposed Morgana. Whilst Cenred's men lay siege to the castle, Morgana uses a rowan wood magic staff to create an army of sword-wielding skeletons to fight the knights inside Camelot. Merlin destroys the staff, the skeletons disintegrate and, as the tide turns in favour of Camelot, Cenred calls off his siege. Morgana, however, takes the credit for destroying the spell and is acclaimed by her foolish guardian.

Merlin finds a secret chamber and accidentally releases a Goblin, which wreaks havoc.

A heroic stranger causes trouble for Merlin after risking his life to save Arthur.

Fleeing enemies, Merlin and Arthur take refuge in The Valley of the Fallen Kings. There, the sorcerer Taliesin cures the wounded Arthur and shows Merlin the Crystal Cave, which provides a disturbing vision of the future in which Morgana stabs a sleeping Uther. Come her birthday, Morgana, given a dagger by Arthur, steals into the king's room to kill, secretly followed by Merlin, who uses magic to thwart her. She is temporarily put into a coma, during which time Uther confides in Gaius that she is his natural daughter - a fact of which she is also aware. Gaius believes that Arthur should be told as now Morgana is a legitimate heir to throne and he stands in her way.

Arthur is pressured into an arranged marriage with a visiting princess, but there's more to her than mere gracelessness and a taste for frogs.

Gwen faces an impossible dilemma when she is forced to choose between saving the life of her estranged brother (Elyan) or Arthur.

Arthur must journey alone to seek out an ancient sorcerer, the Fisher King, and retrieve a golden trident to prove his right to the throne. Morgana gives him an amulet, the Eye of the Phoenix, which will weaken and kill him if worn for too long. Discovering this, Merlin sets out after him, collecting Gwaine, and they save the debilitated prince from two attacking wyverns, discarding the amulet. Arthur believes the quest is his but Merlin, separated from the others, meets the Fisher King, who tells him he is the chosen one. He gives him a bottle of water from the lake of Avalon to use if Camelot is in peril. The quest is accomplished but Guinevere has also discovered that Morgana is a baleful sorceress and confides in Gaius.

A healer is in Camelot using magic to heal the sick, and Gaius quickly realizes it is Alice, a woman whom he was about to marry many years earlier until she had to flee from Uther's persecution of sorcerers. Now Gaius is happy to work with Alice again in preparing potions, but he is unaware that Alice is being controlled by a mythical monster, a manticore, which urges her to poison the cold-hearted king. To break the manticore's hold over Alice and ultimately save her from execution, Gaius has to perform the magic that he possessed but had forsaken long ago.

Prophetic dreams of Guinevere becoming Camelot's Queen torment Morgana. Morgause encourages her to reveal Arthur and Gwen's courtship to Uther, knowing the king will do whatever it takes to stop his son from marrying a serving girl. As a result, Uther banishes Gwen from the kingdom, forcing Arthur to make the ultimate sacrifice of leaving Camelot to join her. Determined to stop the loving couple, Morgana frames Gwen for the unpardonable crime of enchanting the prince. With destiny once again at stake, Merlin will be compelled to risk everything to save Gwen from a gruesome death.

Camelot's legendary tournament only has one rule: there are no rules whatsoever. Terrifying warriors start to fill the mythical city, Gilli amongst them. Despite his small stature, Gilli is ready to join the action and committed to achieve victory with a secret weapon to help him: magic. When Gilli begins to realize the full extent of his powers, Merlin becomes torn since his new friend is putting his own life in danger as well as threatening the very heart of Camelot with his actions. Will Merlin be able to make Gilli see sense before it's too late?

Sir Leon is nursed back to health by Druids using the Cup of Life after he is the sole survivor of an attack by Cenred's men. It purportedly grants immortality to those who drink from it, and Arthur and Merlin retrieve it from the Druids to prevent it falling into Cenred's hands. However, they, along with Gwaine, are ambushed and the cup stolen. Having killed Cenred, Morgause makes his soldiers drink from it and, under her orders, they successfully attack Camelot. By the time the three young men arrive back at the court, Uther is in chains and Camelot has a new ruler.

The new queen of Camelot proves to be far crueler than Uther, who is made to watch from his dungeon as she slaughters innocents. Guinevere helps Sir Leon escape from prison and joins her brother Elyan, Gaius, Merlin, Arthur and Gwaine, who are hiding in the woods. Soldiers follow but they are saved by Lancelot and a youth of immense strength, Percival. Merlin looks into the waters of Avalon in the phial given him by the Fisher King, which directs him to Excalibur, the sword which will defeat the enemy. The fugitives find a round table, around which they movingly declare allegiance to each other, and Arthur knights all the young men - except, of course, Merlin, though Lancelot, aware of his powers, tells Merlin he is the bravest of them all. The group launches its invasion of Camelot, which gives Gaius his finest hour as the sisters are routed, largely due to Merlin's use of Excalibur. However, he places the sword in a rock until it can be used again.