The Doctor used his sonic to drop a drone on the Flix's head. It was surprisingly heavy and knocked the alien unconscious. The Doctor stood a respectful distance from the grieving prince and thought, That boy sacrificed everything for us. (- Italicize this). Now they didn't have to worry for the future, since the aliens' plan was crumbling apart...but Arthur had lost the man he loved.
And that impacted the future. There would be no Merlin standing faithfully by the king, two sides of the same coin, ruling fairly and justly.
He had to try to save the wizard.
Kneeling respectfully, he pulled out his sonic and was about to scan the boy when Amy and Rory turned the corner.
"What happened?" Amy cried. The Ponds rushed forward.
"Ah, Rory the Roman is a nurse!" the Doctor remembered, slapping his forehead. "Rory, come here. Amy, grab the tassel off that drape and help me tie him up."
Rory knelt by the blond, asking "What happened?" as he got to work.
"He-he was..." The prince could find no words to describe what had happened to his friend. A metal ball had thrown a beam of red light that had killed Merlin. Before, he would have called that sorcery. Now, after meeting the Doctor, he wasn't so sure.
"He was shot by a drone," the Doctor informed him.
Rory placed a couple of fingers on the side of Merlin's neck. The moments stretched on, second by agonizing second.
"He's got a pulse!"

With Amy securing the Flinx and propping him up against the side wall, the rest of the gang bustled about Merlin's body, slipping a balled up curtain beneath his head before Rory attempted CPR. Arthur sat back, stunned. He'd never seen someone try to revive an unconscious person this way, and for a moment he thought the man would crush Merlin's ribs. However, the air in Merlin's lungs started moving again. He snapped back to reality, wailing in pain, Rory tightening the fasten over his upper shoulder.
"It missed your heart by inches. You're lucky."
Arthur reached to hug the boy before he remembered his injuries, fighting against himself. "I'm forever thankful sir."
Rory nodded, "Being personally thanked by prince Arthur... I think that's a step up from putting Hitler in the cupboard."

The Doctor grinned, "I married the queen. Beat that."
Amy wandered over, taking her place at Rory's side happily before smiling down at the scene. The blow had rendered Merlin unconscious, and knocked the wind from his lungs. All he needed now was some proper treatment, and time. Amy once more grabbed her husband's hand, placing a light kiss on his cheek.

Peace restored, the Ponds helped drag the Flinx into the T.A.R.D.I.S. Arthur helping Merlin along the path as they conversed with The Doctor. Merlin was the first to question, "What about Opic?"

"He and his men are in violation of the laws of the Shadow Proclamation. We'll take this one to their headquarters and the matter will dispose of itself. Until that time, you and Arthur need to remain safe. It shouldn't be too long, or that difficult, but be on lookout none the less." he informed.

The prince and his wizard waved goodbye before sharing a passionate kiss, Arthur propping Merlin up over his own body, never letting him fall. Amy and Rory followed their example, and shared their own. The Doctor smiled. Saving the day was his specialty. Meeting Arthur was a treat as well. He and Merlin, a love to outlast time.

Just this once, everybody lives.