Merlin wasn't always immortal, nor did he always possess magic. Before the age of Arthur (1,000 years ago), Merlin drank from the Holy Grail, which didn't just quench his thirst. The cup transformed him into one of the most powerful wizards to ever live.
To forge Excalibur and the dagger, the flame of Prometheus is needed, because it's heat is the one that created Excalibur in the first place. Actually, the original Dark One took Prometheus in the form of an ember. As showcased in the episode, Emma got the ember back. However, back in present day Storybrooke, Emma used it to make Excalibur whole again. I have a feeling bad things are ahead for Storybrooke and lightness.
In Camelot, Merlin told Emma that the Dark One is capable of killing him, despite him being immortal. Also, if he dies, it is because of Emma, because she succumbed to the Darkness and became the most powerful Dark One ever in existence.
As many fans previously guessed, Nimue turned out to be Merlin's one true love and the original Dark One. After drinking from the Holy Grail and becoming immortal like Merlin, Nimue crushed Vortigen's heart (the man who destroyed her village) and turned dark. She's also the one responsible for breaking Excalibur into two.
Not only did Merlin create Excalibur, but he also made the dagger. He forged Excalibur by melting the Holy Grail. His hopes were to create a sword so powerful that it would strip him of his immortality and magic, which would lead to a normal life with Nimue. Obviously, that's not how things went. After Nimue broke Excalibur, Merlin created the dagger as a way to control Nimue/the Dark One. He and his apprentice also ensured Excalibur's safety by putting it inside the stone.
Despite making the dagger, somehow Nimue got control of it and placed Merlin inside the tree.
See? There's so much more to Merlin than his magical abilities.
Once Upon a Time airs Sundays at 8/7c on ABC.
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