Years before Arthur, there are two men running through the desert (one of which is Merlin). They see something in the sand and Merlin recognizes it as a goblet (with a cross on the side). His friend claims it as a gift from the gods and picks it up and turns to dust. Merlin prepares for the same, but he asks the heavens for permission first. He drinks from the cup and the desert turns to lush greens and he has his powers.
Merlin uses his magic for good to heal and help people which is how he meets Nimue. Nimue came to Merlin after a Dark One, Vortigan, destroyed her village. Merlin falls for her. They spend time in her village watching the flowers grow when she asks him why he hasn’t proposed to her yet. Merlin tells her about the Holy Grail 500 years ago and it gave him eternal life and magic. If he marries Nimue, it means he will have to watch her die.
Merlin tells her the Grail is still there in her village and she realizes if she drinks from it they can live together forever. Merlin suggests they make the Grail into a sword and they can use it to abolish immortality and live a life of happiness together. Merlin takes some leaves from a flower and turns it into a ring.
They go back to her village to get the Grail and find it in ruins. Merlin finds cups scattered on the ground and realizes the Dark One is looking for the Holy Grail. He has a vision that the Dark One is near by.
Merlin turns the goblet into a sword when the Dark One shows up and attacks Nimue. She tries to fight him, but he stabs her. Merlin sees her die in his arms and prepares to face off with the Dark One. Nimue sneaks behind him and takes his heart. We find out that she drank from the Grail when Merlin wasn’t looking. Merlin tries to talk her out of killing the Dark One because he knows what will happen if she does. She is blinded by revenge and crushes his heart. The flame goes out and she becomes the true Dark One. She then breaks the sword in half.
Merlin tells the group that they can save Emma by putting the blades back together, but they have to get the Flame of Prometheus, which was used to forge Excalibur. The problem is the flame was technically extinguished but still exists as an ember in the possession of the first Dark One. Merlin warns her that the first Dark One is powerful and has the power to kill Merlin.
Emma shares a moment with Hook, who gives her a good-luck ring because while the Dark One is immortal, Emma isn’t.
The rest of the group is trying to figure out how to break into the castle so they can steal the sword and dagger back. Zelena forces Regina to remove her mute spell and she helps them by giving them a way into the castle. But in return for helping she wants her magic back.
Emma and Merlin talk on their walk through the forest about the darkness. Emma wants to know if there is any hope for her because she thinks the darkness is winning. Merlin believes there is hope. They arrive at the Flame and he gives Emma the dagger. She needs to call on the power of the object to talk to the previous Dark Ones to get the ember back. Names cycle on the dagger and then Nimue appears. She tries to convince Emma that love isn’t as powerful as she thinks. She forces Emma to try to kill Merlin, while Merlin attempts to get Emma to think clearly. But Nimue pushes too far and Emma fights back. She yells she doesn’t need her power because she isn’t nothing. The dagger goes back to Emma’s name and she takes the ember.
When Emma asks what happened all those years ago, Merlin tells Nimue put him in the tree.
The group has managed to use what Zelena told them to get into the castle. Snow has to guard Zelena, but she outsmarts her and knocks Snow out. Zelena gets into the castle and reveals that she was working with Arthur. He had removed her cuff and allows her to do magic. She helps him put a spell on the half-sword so it has Merlin’s name. Arthur summons Merlin. Merlin has to do whatever Arthur says. Merlin tries to talk sense into Arthur by saying they can reunite Excalibur, but Arthur is too mad and has Merlin magic the group away.
Rumple tells her it’s time and all the Dark Ones, along with Nimue, show up. She uses the ember to put the sword back together and then flashes back to when Merlin warned her not to take the sword. There is a moment where it seems like she might not take it, but then she does.