I haven't seen any classic Doctor Who, just the 2005 series forward, so please forgive me if this contradicts anything established earlier on. This idea just bit me the other day while I was watching "The Doctor's Daughter," and wouldn't let go.
Cause and Affect
O the suns, they shall weep for the tragedy,
And the stars as they wheel through the sky,
That the beacon of hope should be hopeless;
That the bringer of death should not die.
–Ancient Gallifreyan prophecy
Donna Noble hummed contentedly to herself as she wandered into the control room of the TARDIS, a fresh cup of tea warming her hands. Another civilization saved. Martha had gone home. It was just her and The Doctor again.
Where was he, anyway? It was too quiet in here, the only sound the raspy wheeze of the engines as they rode the Time Vortex.
Oh, there he was—just round the other side of the central console, slumped in the wide chair. "Oi! Spaceman!" she called out cheerfully. "Fall asleep at the controls? Where are we off to next?"
Donna thought The Doctor was hilarious when he was startled—all flailing, spindly arms and legs, his voice going up a full octave. But none of that happened now. He barely twitched as her voice shattered the near-silence, then slowly looked up to meet her gaze. "Donna," he croaked hoarsely.
Donna set down her tea and hurried to his side. "Doctor, are you all right?" she asked gently, knowing full well that he wasn't. She hadn't expected him to be unaffected by the events of the day; she was just a little surprised to see him so… so…
Broken. That was the word. And it tore at her heart to see him this way.
And yet he tried to reassure her. "I'm always all right," he said with a pathetic attempt at a smile.
"No, you're not. Budge up," Donna said, and sat down beside him when he made room. "Now, tell me what's going on in that enigmatic alien head of yours."
The Doctor sighed, sniffled, and wiped tears from his red-rimmed eyes before they could fall. "I didn't want to get close to her," he said softly. "I didn't want to think of her as my daughter, so I tried to push her away. I tried so hard, Donna, but I couldn't do it."
"But why? Why even try?"
"Because she was a soldier!" The Doctor's breath was hissing through his clenched teeth, and the pitch of his voice was starting to rise. He pushed himself out of the chair and started to pace. "I've seen more wars than I can count. I fought in the Time War. I've been a soldier. I know what happens, all too often, to soldiers." He stopped pacing and stared at her, drawing in another shuddering breath. "I couldn't stand to go through that again."
"Again?" Donna repeated, momentarily puzzled. Then The Doctor's voice echoed in her memory: I've been a father before… I lost all that a long time ago. "Oh, Doctor…" she whispered.
The Doctor leaned against the console so he was half sitting on it, his long arms holding him more or less upright. The same casual posture Donna had seen so many times before became one of utter dejection as he hung his head in despair. All the anger he'd been biting back evaporated, leaving his voice inflectionless as he whispered, "I fought in the Time War—and so did my children."
Donna felt vaguely ill. There was only one place this story could be going.
"I was so proud of them when they joined the military. Following in Dear Old Dad's footsteps," he said bitterly. "Adastra—my daughter—was the pride of the starfighter fleet, the best pilot Gallifrey had seen in decades. And her brother Cernunn, oh, he was a brilliant gunner, just brilliant. The pair of them alone terrorized the Dalek fleet." He sucked in another hissing breath and stared up at the ceiling. "I was their commander at the Fall of Arcadia. I ordered their unit into battle… and they were ambushed. The Daleks had hidden an overwhelming force a second out of sync, and as soon as our fighters were launched, they pounced. They annihilated our fleet almost instantaneously. I watched my son and daughter die in fire and screams and silence. By my own orders."
A question slipped past Donna's lips before she could stop it. "What about their mother?"
The Doctor fixed Donna with a bleak stare. "I deserted at Arcadia. Stole a TARDIS and ran back to Gallifrey. Where I ended the war once and for all." A single tear slipped down his cheek. Donna didn't think he even noticed. "She wouldn't leave the planet. 'Do what needs to be done,' she said, and then she burned with Gallifrey." The Doctor turned his back to Donna, bent with grief and shame. "I keep talking about how I've lost everything, but that makes me sound like a victim. Truth is…" He looked at Donna with wide, horrified eyes, the thought occurring to him even as he spoke it. "I've destroyed everything—and everyone—I've ever loved. All this time I've spent railing and raging against my terrible fate, and it was my own doing all along."
Donna was on her feet in an instant, resting a comforting hand on his back as she said softly, "Oh, come on now, you can't go blaming yourself for all that."
"Can't I? Why do you think I don't carry weapons? I'm dangerous enough as it is. Maybe the Daleks were right in calling me 'The Oncoming Storm.' I leave enough death and destruction in my wake, why not?"
"Doctor, listen to me," Donna said firmly, fighting back tears of her own. "Just answer me this: your children, Adastra and Cernunn—did you make them join the military?"
"What? No, of course not. It was their own choice."
"And they knew what the consequences could be?"
The Doctor sighed and sagged under her hand. "Yes. Yes, I suppose they did." He straightened and turned to face her, his eyes pleading, heartbroken. "But what about Jenny? What choice did she have?"
"She chose to save your life!"
"Cobb would have to be a bloody good shot to kill a Time Lord with one bullet."
"Oi!" Donna smacked him on the shoulder. "Don't you start pulling the almighty-Spaceman business on me, Spaceman. You're missing the point!"
"Oh, yeah?" snapped The Doctor, the anger returning. "And what would that be?"
"That they all trusted you!" Donna fired back. "They trusted you to see the bigger picture, to do what needed to be done. They trusted you to save the world, even if they couldn't be saved." Her voice softened. "You inspire people, Doctor. There are people out there who are not just alive, but, stronger, braver, better, because of you. You bring them hope, you fill them with courage." She looked up into his face, her eyes shining. "Doctor, you're the rallying point for the entire Universe. They all believe in you."
The Doctor was silent, stunned.
Donna stepped closer and took him by the shoulders, gazing into his eyes. "I know you've just lost another child. I know it hurts. I can't even imagine the pain you're in right now. But don't lose sight of that bigger picture, Doctor. The Universe needs you. I need you."
The Doctor blinked once. "Right, then." Then he grinned and jumped back, dancing around the TARDIS controls with that animation that Donna found so painful to watch, knowing as she did what it was meant to disguise. "Right then, let's see where we're needed now!" He yanked the TARDIS out of the Time Vortex and started to bring it in for a landing. "Allons-y!"