Chapter Warning: I'm sorry. More than I can say. I am so, so sorry.
He pushed those thoughts to the back of his mind and stepped out of the box, looking around. The warehouse was extremely abandoned with no bulbs in the light sockets and no equipment of any kind to be found. Only large, rusting metal containers remained, many with no lids or doors. The ceiling far above him was dotted with peeling paint. The air smelled of must and rat droppings. He wrinkled his nose in distaste.
Suddenly, the Time Lord heard the scuffle of running feet and a voice panting with fatigue. He pushed his way through the tiny opening between two containers. "You let him go right now!"
Donna!
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Emerging from between the crates, the Doctor saw a horrifying scene unfolding in front of him.
On one side of the open expanse in the warehouse stood Donna, holding her grandfather's pistol and looking quite cross doing it. Her hair was sticking her to face and neck, sweat from some physical exertion that the Doctor hadn't seen. His best guess was that she had managed to wrestle herself away from Kovarian, who then turned on her grandfather and took him hostage.
Kovarian and Wilfred were on the other side of the expansive warehouse, to the Doctor's left. Madame Kovarian had Wilfred in a very scary and precarious position. Her blaster was pressed to his throat and he was watching Donna nervously. The Doctor saw a wave of relief flood his features when the Time Lord stepped into view. "Doctor! She-"
"Quiet!" Kovarian hissed. Her normally crisp composure was frayed at the edges, showing a dangerous woman ready to kill at a moment's notice. She pressed the gun further into Wilfred's jugular.
"Madame Kovarian, so nice to see you again," the Doctor said amicably. "Fixed your vortex manipulator, did you? It doesn't go very far though, I see."
She clenched her teeth in annoyance. "You left enough pieces behind that it could be repaired, for short trips at least. Several time hops later, here I am."
"Time what?" Donna demanded, taking a step toward the woman who had her grandfather at blaster-point. "Listen up, Nazi Pirate! You let my gramps go right now or I am going to shove this gun right up your-"
"Oh you would say that," the Doctor interjected, walking carefully over to the ginger woman. She eyed him suspiciously. "Not that the gun can shoot bullets or anything."
"And who do you think you are?" she asked angrily. "This... This bitch killed my husband!" The Doctor could tell that her anger was the only thing keeping her from breaking down in hysterical tears.
His voice softened. "I know Donna. It's all my fault and I am so, so sorry."
"What do you mean your fault?" Her focus was momentarily on the crazy man with the bow tie. "How can it be your fault?"
"Long story, explain later." The Doctor fished the sonic screwdriver from his jacket pocket and aimed for Kovarian's blaster. Unfortunately, nothing happened. The Doctor balked. "You put a dead lock on the gun?" he asked incredulously.
Kovarian allowed herself a smirk. "Anything to frustrate and irritate you, Doctor." She said his name with as much deadly venom as a black mamba.
"Why did you want Donna?" he asked quickly, sending the ginger woman a signal to shut her mouth and keep it that way for more than two seconds.
Kovarian's smug expression broadened. "We mapped the child's timeline to the day you erased her mind. We saw what she would become, the knowledge that she would possess. We let you take her back then in order to take her now."
"But what for?"
"The knowledge of the last Time Lord is the most precious commodity in the universe, Doctor. Even you should know that. I could drive planets and species into the ground at a simple word, destroy and re-shape the universe to my own design. Destroy you."
"Oh, it's always about taking over the universe, isn't it? Does no one ever stop to think that maybe the universe doesn't like you?" The Doctor quickly ran a hand through his hair, then glanced at the woman standing only a few feet away from him. "Donna, I've got a plan, but you have to trust me."
"Why should I trust you, you said this was your fault! And what's this about erasing my brain?" she yelled, gripping the gun in her hand with white knuckles. Wilfred stayed silent, but watched the two carefully, hoping that the Doctor had a damn good plan. He mouthed 'trust him' to Donna, but she didn't see it.
"Donna, think back to when you were seven years old. There was a man, he took you to the orphanage, but then he came back. You saw him on a playground, you were wearing a red dress-"
Donna glanced at him out of the corner of her eye. "What are you talking about?"
"Remember, Donna. You have to remember. That's the only way I can get you to trust me." He eyed her in return. "You know me."
"I don't," she replied immediately. Her gaze was locked on her grandfather, but he saw the recognition in her bright eyes.
He let the faintest smile grace his lips. "Yes you do, and you remember. You have to trust me."
She shifted her gaze and stared at him for a long moment, then nodded. "Okay. I trust you."
"Good-"
The crack of Kovarian's blaster shattered the almost silence of the warehouse.
The Doctor caught Donna as she fell, suddenly in a state of shock from the blaster shot that was now burning in her ribcage. Wilfred yelled in desperation as his pistol clattered to the floor at his granddaughter's feet. She gasped for air, holding a hand to the gushing wound. The Doctor panicked and pressed her hand harder to the area, trying to stem the flow of blood. He barely heard Wilfred's voice and Madame Kovarian's self important monologue in the background. All he could think about was his best friend and the fact that she was dying.
"Donna! Donna, listen to me." He lowered her to the floor, where she lay writhing in pain. She was having trouble breathing, which indicated to him that the shot had pierced her lung. He could have cursed in a million languages. Half Time Lord or not, she couldn't survive that.
"She is a weapon, Doctor! Nothing more! And I will have her!" Kovarian announced triumphantly. She was confident that causing the ginger woman to regenerate would restore her memory to before she became Donna Noble. She would once again be Melody Pond, living the life before she was tainted with all of the precious, altruistic ideals that Earth humans possessed and coveted. Her Time Lord mind would stay carefully tucked away, ready for excavation at a moment's notice.
The Doctor gritted his teeth, knowing that Kovarian was not leaving without her prize, then turned his attention from the evil woman and Wilfred to Donna once more. "Donna, please listen to me."
"It... It hurts..." she gasped, breathing shallow. He felt his hearts break, but pressed on.
"Donna, you have to regenerate. You have to do it yourself, it's not automatic, please." He grabbed her free hand to focus her.
She managed to gaze at him through the sweat on her brow. "Re-what?" She groaned, skin becoming more white by the second.
"You know how to do this, you've done it before. Please, Donna." A thought suddenly hit him and he grasped her hand tighter. "I'm the Doctor. For once, you have to remember. Remember all the times we ran. We ran and we met Agatha Christie! We fought Sontarans and the Daleks. You saved the universe. Twenty seven planets and billions of people. You have to remember."
She gazed at him for several seconds before blinking. "Doc... tor?" She lifted her bloodstained hand to touch his face. Before the contact was made, the Time Lord saw the beginnings of her regeneration in that hand, golden artron energy swirling down her arm in the most beautiful designs. He felt a surge of hope and let go of her other hand, standing up and away from her. He knew what Kovarian was planning, but he also knew one other thing.
Nothing would be the same ever again.
Donna's body convulsed one last time as the regeneration completely took over. The Doctor did not shield his eyes from it, but revelled in the answers he was about to receive. Wilfred was shouting from his place near Madame Kovarian, but the Doctor didn't hear him.
As the golden light faded, he gazed down with a goofy grin at none other than River Song.
She slowly opened her eyes, seeing the Doctor first and foremost. She said nothing, but carefully sat up, eyes glued to Kovarian and Wilfred. The Doctor began to help her up, but she pushed him away. He frowned, but let her stand on her own. She slowly struggled to her feet, dizzy from the regeneration. The Doctor didn't notice her lift the pistol from the ground and clasp it tightly to her side.
Madame Kovarian looked utterly horrified, for lack of a better phrase. They hadn't had any time to measure the baby's timeline this far; through Donna's memory wipe had taken the month that they had in Nazi Germany. There were legends about this woman and her exploits. The dreaded River Song, adventurer and companion of the Doctor. And now River was here, all because of her.
The Doctor was absolutely giddy, despite the situation. He looked rather smug, standing next to River and feeling rather self-important. This was the youngest River that would ever be and she looked somewhere around her early twenties, in human years. "Hello," he said with a grin.
The curly haired woman glanced sideways at him, then in a single swift movement, raised the pistol and fired.
The metal bullet hit Madame Kovarian's hand, causing the bones to splinter and her blaster to fall to the floor. She cursed loudly and Wilfred yelled an exclamation of triumph. He began to run away from her, but Kovarian quickly wrapped her injured arm around his shoulders and raised an object in her opposite hand to his neck. "If you shoot again, I'll inject him with this."
The Doctor squinted, as it was hard to see in the half-darkness of the warehouse. "What is it?" he demanded. Any injury she could inflict on him would invariably be cured by the TARDIS if it didn't happen too quickly.
"Karutlil venom," she hissed, pressing the object to Wilfred's jugular.
The Doctor stared, horrified. Karutlil's were extremely rare, poisonous plants found on Pharos 5. They had a large maw rather like a venus fly trap that secreted the most virulent, unique venom in the universe. It was the only poison known that did not have an anti-venom. Its rarity contributed to the lack of a cure, not to mention that it would permanently paralyse a human from head to toe in exactly ten seconds. "You can't-"
"She comes with me, or he suffers," Kovarian spat.
"Don't you dare!" Wilfred yelled, squirming in the woman's grasp, desperate to get free. "Don't you go with her!"
The woman that was now River frowned. She raised the pistol again, taking careful aim, but there was no way to shoot Kovarian without hitting Wilfred as well. That would be a bit counter-productive.
The Doctor scratched at his head briefly. This was becoming more of a stalemate every second. Madame Kovarian would not leave without River and she would kill Wilfred if the woman refused. The Doctor couldn't do anything without Wilfred being poisoned.
Madame Kovarian eyed the blaster near her feet, looking as though she wanted to pick it up again. She carefully began to bend over to snatch it up, but Wilfred caught her in time and kicked the device away.
That was the woman's breaking point. Frustration at having her plans thwarted, broken vortex manipulators, and the appearance of River Song sent her over the edge. Knowing that she could not truly win this battle now, she let out a cry of rage and stabbed the syringe full of poison into Wilfred's neck.
Wilfred let out a cry of pain and Madame Kovarian stumbled back from the man, which gave River the vantage point that she needed. She raised the pistol and fired twice, sending the metal bullets deep into the evil woman's heart. She fell dead with a dull thud next to the empty syringe.
Wilfred immediately began to breathe heavily, the poison racing through his system. Three seconds had already passed. The Doctor took off running in the man's direction, frantic to get him into the TARDIS. The paralysis would not kill him as long as they transported him to a proper facility in time. He saw Wilfred's face as the man struggled to breathe and stay upright.
Suddenly, the final piece of the puzzle clicked into place. He felt realisation dawn on him, an epiphany so obvious he couldn't believe that he didn't see it before.
"Octavian said you killed a man."
"Yes, I did. A good man. A very good man. The best man I've ever known."
Halfway to Wilfred, the Doctor skidded to a halt, turning back to see River's eyes filled with tears and the pistol raised. His eyes went wide. He screamed.
"NO!"