Theory

Ok what if Merlin didn’t took the darkness out of Emma but instead told everyone the only way to destroy it is to save the original Dark One and the original Dark One is alive and the dark enitiy we saw that almost took Lancelot is the Dark One way of corrupt people to become the Dark One so to get more souls and to be more powerful and everyone decide to have their memories erase so they wouldn’t want to mess up the plan  Emma pretending to be the Dark One with Merlin help and she telling Regina Hook Henry to trust her and Excalibur won’t snuff out the light but destroy the darkness but since darkness can’t completely be destroy everyone decide to get a piece of darkness inside them where they can control it instead other way around.

Because according to legend Merlin love Nivane but she was so afraid that Merlin will use spells on her she ask him to teach her magic but secretly she didn’t love him at all and in the end turn on him since the writers like to twist stories in the show and Nivane really did love Merlin but she was afraid magic would corrupt Merlin so she ask him to teach her so she can protect him but instead it corrupt her and because Merlin was so blind by his love for her he didn’t notice she was started using Dark magic and in the process she turn into the Dark One so Merlin defeat her by sending her to Mist of Avalon and to make sure to keep her there Merlin created Excalibur and broke it in half to create the dagger to control her but Merlin was so impatient he try to save her himself but instead couldn’t kill her and this is why he became a tree and since we know Merlin can see bits of the future he thought Arthur will be the true hero that can help him destroy the darkness but was wrong and Merlin realize he needs not only Emma but everyone to help him. I don’t know just a thought.