The Doctor laid Donna down gently onto the metal grating of the TARDIS floor. He had entered her mind and for a moment was about to do something even he found unthinkable. But at the last moment, he changed tactics and essentially put her into a coma. Now she lay on the TARDIS floor and he paced around the console in circles. "Think, think, THINK!" he started grumbling at himself, but it turned a full yell as he pounded his fist into the side of his head.
"She's part Time Lord, but not enough. She can't handle all that Time Lord information. Do I take away her memories?" He paused his pacing to look down at the woman who lay in front of him. "Argh! No! I can't do that. She'd as soon die as forget about this life." He continued pacing. "The Chameleon Arch! Maybe if I alter it we can remove the Time Lord parts without removing all her memories—" He thought for a moment longer about that option. "Grr! No, too big a chance at total memory loss, and once again, not what she'd want." He kept pacing around the console, mumbling to himself as thoughts flew through his mind, coming out verbally in bits of pieces. "Part Time Lord. Part Human. Time Lord consciousness. Human body. Incompatible. DNA. Rewrite. Can't go back to human without memory loss—go back—can't go back—go—forward?" He stopped, turning and looking up at the time rotor as he shouted, "That's it!"
He ran around the console, setting his coordinates, then ran over to the monitor, punching in a number. A moment later, Jack's face came across the screen. "Jack! I need you!" Before Jack could even manage a witty retort, the Doctor continued yelling, "Remember when we first met!? Remember those nanogenes? I know you have some of those hanging about someplace at Torchwood." The Doctor saw the denial coming a mile away and stopped him from talking. "No, don't argue! I need them! Now!"
The Doctor pulled the lever and held on tight, the TARDIS flew through the vortex and found herself materializing inside the Torchwood Hub. Jack came running up to the doors, holding a clear glass container that seemed to glow from thousands of little lights inside. Just as he made it to the doors, they opened and the Doctor was there waiting. He pulled the man inside by the arm and slammed the doors shut.
"Alright, Jack, no time to explain." The Doctor ran up the ramp and knelt down to gingerly pick up Donna in his arms, then stood by the console looking down at her. "I need you to open the jar. The nanogenes should sort out the rest."
"But Doc—"
"Jack, it's the only way she'll survive," the Doctor pleaded with his friend, both in his voice and his desperate expression. "I can't take her memories away, I can't make her live a life where she forgets about me, where I'm supposed to move on without her. She wanted forever with me, I promised her forever, and if this is how it happens, then I won't let you—anyone—stop it."
"Okay—okay, Doc. I get it." Jack let out a deep breath and twisted the top of the container loose. He took one last look at the Doctor, who nodded to him, before he pulled the top of the container off.
The glowing nanogenes flew up out of the container, momentarily spinning in place between Jack and the Doctor, before rushing towards the Doctor and Donna. They spun around the two bodies for a moment.
"C'mon, c'mon—you're smart, figure it out. Time Lord DNA here, needs to be there for her survival. Make her like me. Make her like me! C'mon!"
As fast as they had spun around the two of them the nanogenes then flew into Donna and her whole body glowed in his arms, then after a few moments, the glowing faded. The Doctor was catching his breath, his hearts still racing, as he lowered himself down onto the floor, kneeling with Donna's head in his lap. He closed his eyes and rested his fingertips on her head, prepared to bring her back out of the coma. Jack was still standing with the container in his hands, not moving a muscle, watching the Time Lord. "Please," the Doctor whispered. "Please, let it have worked." He sat in silence a moment.
"Spaceman?" a whisper broke the quiet. "What happened? What did you do?" At the sound of her voice, tears flowed down his cheeks. He pulled her up and held her tight, allowing the tears to fall.
His best friend, his Donna, was saved.