They're in the courtyard battling each other with the strongest magic they possess when Arthur gets in a lucky shot with his crossbow. He hits her right in the soft space in her throat that Merlin so loved to kiss many years ago. Suddenly, she's choking on her own blood and Merlin has a flashback to when he poisoned her with the hemlock. Has a flashback to when Arthur killed Freya. Her eyes are round, scared, and vulnerable.
Arthur drops the crossbow like he's been burned and he can't believe what he's just done to his sister. To his friend.
Merlin rushes across the courtyard to hold her before she falls. He holds her as she breathes her last bubbling breath and when she dies, Merlin's light dies with her. Hefinally understands what the Dragon meant when he said that she was the darkness to his light. Because without darkness there is no light. Light doesn't mean anything if there's not a darkness. Darkness balances our light.
In his heart of hearts Merlin had always hoped for reconciliation between the two of them. That the love they shared would eventually come back.
Now there can be no reconciliation. Arthur has taken that from him just as Arthur has taken everything from him. Eventually everything falls behind Arthur.
He has spent the best years of his life protecting Arthur, making sure Arthur lives. He has forgotten to bring magic back. He has forgotten what it is to live. He has no family of his own left. Both his mother and father are gone, will is gone, Lancelot is gone, Freya is gone, Gwen has run away to a convent to praise the new God and the new religion from Rome. All he has is Arthur and the secret dream that one day he will have his Morgana back.
Now that dream is bloody on the cobblestones in the courtyard. He thinks how funny it is that the day Arthur finds out that he has magic, that he is Magic incarnate, is the day he doesn't care about Arthur anymore. He can't forgive Arthur for this one.
With nothing left to lose Merlin calls the Great Dragon.