The has been no news on Lady Morgana since she disappeared a year ago. Merlin and Arthur get a lead though but they attacked by some bandits but Merlin's secret magic saves the day. A bruised and bloodied figure approaches the group who turns out to be Lady Morgana. Morgona is welcomed back at Camelot but Merlin is worried she will tells somebody what happened the last time they met. Morgana attempts to convince Merlin that she has changed and insists no one will know what happened. The truth about Morgana is revealed though when she slips out of the castle and meets up with Morgause.

Merlin finds it hard to recover from the serket's poison. Morgana and Morgause step up their plans for the invasion of Camelot whilst he is out of action. Morgause continues to manipulate Cenred, as he prepares to launch an attack on the citadel. Morgana receives a powerfully enchanted rowan staff from Morgause to help her in her magical treachery. King Uther is still not able to rule as he tries to recover from the enchantment. Arthur is left to defend the attack on the citadel. Merlin knows it is down to him to try and stop Morgana without revealing his own powers.

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Merlin and Arthur find themselves outnumbered in a bar fight but an enigmatic young man helps them win. The man's name is Gwaine and he risks his own life to protect Arthur but during his act of bravery he is seriously wounded. The Prince decides to take him back to Camelot where he could make a recovery with Gaius' help. Gwaine immediately gets to work: drinking, flirting with the ladies and causing lots of trouble for Merlin who has been instructed to look after him. However, when two unscrupulous knights seem to plot to murder the Prince, will Merlin and Gwaine be able to stop them and save Arthur?

Merlin meets with the mysterious Taliesin and the old sorcerer takes him to the crystal cave and shows him a glimpse of the future. Merlin sees Morgana who is about to murder Uther. Merlin realizes that it is down to him to make sure that what he saw never happens.

Arthur finds himself being pressured into an arranged marriage with Elena. Merlin soon discovers though that Elena may not be exactly who she claims to be.

Gwen finds herself facing an impossible dilemma when she has to to choose between saving the lives of her estranged brother, Elyan, or Arthur. One of them seems certain to die at the hands of Cenred as Gwen faces an impossible decision.

Arthur leaves on a solitary quest to retrieve the Golden Trident from the Fisher King so that he can prove that he is worthy of being the next king of Camelot. Morgana decides that she has an opportunity to use her dark magic and she ends up gives him a precious bracelet containing a Phoenix Eye which puts him in danger. Merlin with Gwaine's help tries to save Arthur.

Alice, an old flame of Gaius' shows up in Camelot and Merlin is happy to see another side to his mentor. After find out out though that she is under the influence of a Manticore, Merlin ends up having has no choice but to tell Gaius of her evil intentions. Gaius and Merlin end up falling out when Gaius refuses to believe the truth about Alice.

Morgana has dreams about Guinevere becoming Queen of Camelot. Morgause encourages her to reveal Arthur and Gwen's relationship to Uther, who decides to make sure they never marry. Arthur decides to leave with her after his father banishes Gwen from the kingdom. Merlin has to risk everything after Morgana causes more problems for Gwen.

Camelot's legendary tournament has just one rule which is there are no rules. Terrifying warriors fill the city and Gilli decides to join the action. Gilli starts to realise the full potential of his powers which leaves Merlin feeling torn. Gilli is not only putting his own life in danger but his actions threaten to destroy Camelot. Merlin attempts to make Gilli see sense before it is too late.

Merlin and Arthur leave for a dangerous mission to capture the Cup of Life. They end up getting captured by unscrupulous slave trader called Jarl. The cup ends up falling into Morgause's hands. Morgause and Morgana hope they can get rid of Uther once and for all.

Queen Morgana starts a reign of evil over everybody in Camelot. Morgause's immortal army help her keep command and it looks like there is no hope for Uther. Arthur regains his strength and Gwaine, Lancelot, Elyan and Percival attempt to help him with a counter attack. Merlin attempts to help Arthur reclaim Excalibur from the Lake of Avalon before time runs out to save everyone.