1000 years before the Age of Arthur…Merlin and another escaped foot soldier escape into the desert where they find the Holy Grail that turns Merlin’s companion to dust when he touches it. Merlin however, is able to drink from it. Suddenly the desert turns green and becomes a forest.
500 years later, Merlin meets Nimue. Vortican ransacked and burned her entire town. She wants revenge. She wants the seeds she saved from the special middle midst flower to continue to grow. Merlin wants Nimue to stay but for some reason he can’t see her future.
Merlin and Nimue fall in love. He decides to turn the Holy Grail into a sword to take away his immortality so that he can live a normal life with Nimue. Nimue encourages Merlin to kill Vortican but he won’t risk using magic to kill. He turns the Holy Grail into Excalibur when Vortican shows up and kills Nimue.
In Camelot, Merlin hopes to reunite the two blades to help Emma. Emma is making dreamcatcher to pull memories from people. Hook says she can no longer sleep.
Merlin tells Emma that they need the spark from mankind’s original fire is needed to forge Excalibur back together. They will also have to face the original Dark One. He says two paths ahead. On one, Emma resists the darkness and they succeed. In the other, she succumbs to the darkness and Merlin dies. If that happens, Emma will be the Dark One that kills him and the most powerful Dark One there’s ever been.
Hook gives Emma his special ring that he thinks has helped him survive. She says she’s immortal now. Hook points out that the Dark One is immortal but Emma is not. He wants her back.
Emma tells Merlin she’s worried that the darkness is winning. He brings her to where the flame of humanity used to reside before the original Dark One stole it. He holds it as a spark. Emma uses the dagger to find the first Dark One, who is Nimue. Turns out the Nimue drank from the Holy Grail before Merlin turned it into a sword. She faked her death and then killed Vortcan. When she used her magic for evil, she turned into the Dark One and broke the sword.
As the rest of the group attempts to steal Excalibur, Zelena shows them a secret entrance she found while being Regina’s handmaiden but she couldn’t open the iron gate at the end without her magic. Regina takes out the gate and the group heads inside while Snow watches over Zelena who wants her magic restored if her plan works. Before everyone gets back, Zelena overtakes Snow and gets away.
Inside, Arthur has made a spell of a liquid that will reduce people to bones and teeth if it is spilled on them. Zelena partnered with Arthur to turn Excalibur into a way to summon Merlin who then disappears on Emma. Excalibur now controls Merlin and Arthur holds the sword.
In present day Storybrooke, Emma has the dagger and Excalibur. Nimue is there with the rest of the Dark Ones to encourage her to dose the light for good. She forges the sword back into one. As she’s about to grab hold, she remembers Merlin telling her to leave the sword alone as a girl, but she still takes the sword.