Everyone blames Merlin for letting Morgana down and ultimately betraying her, but I think it starts much earlier and that Arthur and Gwen are equally, if not more, responsible. Gaius, too.
From the beginning of season 2, the core trio (Arthur, Merlin, Gwen) is constantly paired off in different combinations. Morgana, noticeably, is not. She’s no longer looped into their dynamic the way she was in season 1. She doesn’t even know about Arthur and Gwen’s growing feelings—and this is before she’s done anything to lose their trust. Nothing about her has changed yet. But for whatever reason, her friends have.
In season 1, Morgana is included. She learns (likely from Arthur) that Merlin offered his life for Gwen in 1x03, and in 1x07 Arthur tells her what he believes “really” happened with Sophia. The first real secret Morgana keeps is her plan to kill Uther in 1x12—but she doesn’t go through with it, and they never find out (except Merlin, who also knows she saved Uther). Then in 1x13, they dismiss her concerns and fear completely. I think that’s the beginning of their collective betrayal.
Also—Morgana explicitly tells Gwen in 1x07 that she’s having prophetic dreams. Gwen reassures her that Uther wouldn’t harm her for having magic. Gwen knows. Gaius knows. Merlin is not the first person Morgana confides in about this. She’s been afraid she has magic since halfway through season 1 for fucks sake.
By season 2, her friends stop showing up for her. They don’t listen, don’t press, don’t support even as she is visibly unraveling. Merlin is actually the exception early on (see 2x03). He tries to help without exposing his own magic, doesn’t dismiss her after their initial conversation, and ultimately sends her to the druids. By the end of that episode, they’ve both essentially acknowledged the truth. Arthur may not know about the magic, but he does know she’s not okay—and still, he’s too consumed by Gwen to really see her. Gaius outright gaslights her. Gwen, despite knowing, offers presence but not real intervention or support.
Merlin is the only one who meaningfully shows up for her—and yes, he later tries to kill her, but that comes after a long stretch of neglect by all of her friends. After 2x03, she’s functionally abandoned. Where is Merlin in 2x07, during the Witchfinder? Where is Gwen? Gwen goes to Gaius, worried Morgana will break—but no one is actually with Morgana, supporting her.
What happened to her friends?
I don't think Merlin poisoning her is the beginning of the betrayal—I think it’s the culmination of her slow exclusion from the group. If they had stayed connected, kept her in the loop, trusted her the ways they once did, they could have protected her—not just from Uther’s emotional and physical abuse, but from her own isolation. From the conditions they helped create that pushed her toward darkness.
If anything, Arthur should have been the one excluded, while Gwen and Merlin protected Morgana and her secret. And Gaius, too.
But, alas, women who are different are always the ones left out. And for her, I truly think it's what made all the difference.
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