A/N So this takes place during The Final Problem. This is what I think really happened so if you haven't seen the new season then don't read this one. I read some theories on Tumblr that I included in here. The theory is that John has lost his eye (due to the fact that little victor -who is pretty obviously a John mirror- wore an eye patch as well as some unusual shots of John's eyes throughout the episode) when he was shot by Eurus and that he is currently in a coma. Another theory I saw is that John was taken prisoner during the war and was tortured (waterboarding) and now has an intense fear of water. (I recommend looking up some of these theories, they are fascinating) Enjoy <3
John's P.O.V
"Let's put a hole in it." The gun went off and John felt the force of the bullet connect with his skull. Pain flowered in his left eye as he hit the floor. He could hear the woman, Eurus, laughing as his vision faded.
"John!" He could hear the familiar voice in the distance, he was so far away. Sherlock, he tried to cry out to his friend, but his thoughts faded away before he could.
Sherlock!
Sherlock's P.O.V
"John!" He stumbled into the room in time to see his friend's body hit the floor. The woman with the gun was laughing as he watched the blood spilling from the open wound on John's face. He felt the blind rage filling his body as he pulled the gun that was concealed in his belt. The woman turned to face him and he felt his stomach drop. Eurus. He remembered her, vague memories from his childhood. The sister they never discussed. She was still laughing, mocking the gun in his hands.
"You wouldn't kill another human being. You are weak, run by your emotions-" He cut her words off with a bullet to the heart. He ran to his friend, inspecting the horrific wound and trying desperately to remember any First Aid he could. Everything was gone; his body was panicking as he tried to find any signs of life in the limp body in his arms. He could hear the sirens as emergency crews pulled up to the house. He heard the sounds of people and he cried out for them as he felt the faint pulse in his flatmates wrist.
"Hold on, John. Hold on for me, please." He whispered in his friend's ear as the people surrounded them. He was pulled away from John, forcing himself to release his jacket as he was stood.
"Sherlock," The familiar voice of the Detective Inspector cut through Sherlock's frazzled thoughts. "Sherlock, what happened? Are you hit?" He felt hands on his shoulders and forced his eyes from John's body. Lestrade was close, way closer than he would normally allow him to be. But right now he couldn't bring himself to care. Lestrade was still asking if he was hit. Why would he ask that? He looked down and saw the blood. John's blood, his clothes were stained with it. He felt his chest tighten and his breathing quickened.
"John," his voice cracked, "she shot John." He was feeling dizzy. Lestrade's face fell and he pulled Sherlock in for a hug, trying to calm the taller man. Sherlock allowed himself to be held by the DI, using the other man's strength to ground himself. The medics started to remove John from the floor and haul him to the ambulance. Sherlock rode to the hospital with him, refusing to leave his side.
John's P.O.V
Sherlock wanted to talk to Mycroft, so John convinced him to really freak him out. Something was wrong though, nothing felt right. Everything was just slightly wrong. Something had happened, but Sherlock was racing from Mycroft's house and John had to follow. They had to find this Eurus. She shot John, but just with a tranquilizer.
Sherlock's P.O.V
The machines incessant beeping was keeping Sherlock awake. Each ping a harsh reminder that his friend was being kept alive by these offending devices. He looked at the still form on the bed, once more trying to will the body to consciousness. For more than a week he had sat like this, watching as he beloved friend deteriorated before his eyes. There were bandages covering the left half of his face, but Sherlock could still see the gaping hole when he closed his eyes. The bullet had hit him at an angle, narrowly missing his brain but destroying the eye. He was lucky, that is what everyone kept saying. If he were truly lucky he wouldn't be lying in the hospital. Sherlock couldn't help thinking this.