A/N: So, I always wanted Jenny to come back and I was watching 'The Doctor's Daughter' again and it struck me suddenly that she's just a baby and if she ever found her dad again, there would be some major problems that would need to be worked out. Anyway, this is my take on things :DOh, and also, the conflict at the beginning was just a convenient way for them to meet. It's not a huge plot twisting thing that will blow your mind or anything.

Disclaimer: I disclaim anything you recognize.

The Doctor wandered through the hallway of the enormous ship. It was more like a small portable fortress than a spaceship. The TARDIS had landed on the planet without his direction so the Doctor had decided to look around a bit. It wasn't like he had anything else to do anyway. In a very short time (because he was the Doctor and it was trouble) he had discovered a very large, very illegal mining operation. The amount of raw materials and minerals that was being extricated was far above the universal "safe" level as decreed by the Shadow Proclamation. At this rate, the planet would be depleted before it could rejuvenate.

Finding a screen set into the wall, the Doctor pulled out his glasses and slipped them on.

"Well, where's all this material going, hm?" He soniced the screen and a three-dimensional paradigm of the mining beamed out along with a running description of all operation statistics. The Doctor's eyebrows shot up and he let out a low whistle at the export numbers.

There was every possibility that the miners had no idea that their numbers were so high. With that thought, the Doctor soniced the screen once more, trying to access the controls of the digging machinery. If he could jam them, then he could try to reason with the company before they were arrested. Suddenly the screen flashed red and a siren began to wail.

"Intruder in section three," a mechanical voice intoned. "Intruder in section three."

The sound of heavy running footsteps echoed down the corridor and a few soldiers appeared on either side of the Doctor, all holding guns.

The Doctor put his hands up. "Now, fellas, just one sec–oof!" One of the soldiers slammed the Doctor in the head, with the butt of his gun and the Doctor collapsed, unconscious. The men unceremoniously dragged him away.

The Doctor slowly became aware of a hard, cold surface beneath his cheek. He blinked slowly, wincing at the pain in his head. It felt like, like –

"You hit me!" he said indignantly, rising from where he'd been lying on the floor and glaring at the men. The soldiers around him gave no acknowledgement that they'd heard him.

"Welcome back to the land of the living," a woman's clipped voice said and he turned to see a severe looking woman, perhaps forty years of age, dressed in an unflattering formal black pantsuit with her hair pulled back into a boring bun. Her thin lips were pressed together as she regarded the Doctor with disdain. "Dr. Jean Everett. Who exactly are you?"

"I'm the Doctor," he replied, a bit pompously.

She did not seem amused. "I don't think so. No, I think that I am the doctor here. Now, why were you trying to break into our security protocols?"

"I wanted to get your attention," the Doctor replied simply.

Dr. Everett sat down behind her desk. "You have it." She folded her hands on the table top and waited.

"Your mining numbers are far, far beyond what's accepted," the Doctor told her. "If the Shadow Proclamation find out, they'll arrest you and shut this entire company down. So, if you don't want that to happen, I suggest you slow things down a bit."

Dr. Everett let out a laugh. "I'm supposed to believe that you came to sabotage my operation out of the goodness of your heart?" The Doctor stared at her in confusion.

"You do know what the Shadow Proclamation is, right?" he asked. It wasn't like he had the highest respect for the Judoon's methods, but they were intimidating. He would give them that.

She scoffed. "Those stupid, hulking rhinos? They don't scare me. Anyway, what they don't know won't hurt them. In fact," she turned to him, suddenly interested. "The only way they would find out is if you told them. Hold him!" The Doctor was roughly grabbed and his arms twisted behind him.
"Ouch! Watch it!" he growled. "What do you even need all this stuff for anyway?"

"Oh, like you don't know, Doctor," Dr. Everett mocked. "This planet is rich with rare minerals. We mine them at a relatively low cost and sell them for a profit. There are wealthy buyers out there willing to pay fortunes for a scrap of this stuff. It's a good business." She shrugged nonchalantly. "One more thing, where are your friends?"

"Friends?" the Doctor asked, confused. "I'm alone."

She cocked an eyebrow, laughing derisively. "Oh, come now. One doesn't launch a plot to sabotage a huge operation without some backup." The Doctor shook his head. "Protest all you like. You can't protect them. We'll find them." She waved her hand dismissively.

The guards hauled the Doctor away to a prison cell in the depths of the ship. Throwing him inside, the door was slammed in his face. The Doctor whipped out his sonic screwdriver immediately. It was lucky they hadn't thought to search him. Explaining his bigger-on-the-inside pockets would have been annoying.

He held the glowing end against the door. Nothing.

"Oh you've got to be kidding me!" he muttered, trying again. The door was deadlock sealed. He kicked it angrily before stomping off to the opposite wall and sliding down to sit on the floor. He shrugged off his coat and began to look through the pockets for something – anything – that would get him out of here.

A pear, horrible thing – maybe he could throw it at someone. That sounded promising.

A banana, much better. He ate it quickly before tossing the peel onto the pear. He could throw that too.

Martha's cell phone. Useful, but not right now. He wasn't even sure what planet he was on after all.

An old copy of Murder on the Orient Express. He'd meant to get it signed but things always got in the way, like giant wasps and amnesia for instance.

A box of chocolates. Blimey, why did he have so much food in here? It was lucky his pockets kept everything in stasis otherwise the Coat would be smelling quite odd by now.

A bigger-on-the-inside bag full of cosmetics and clothing. Oh yes, Rose had made him pack an emergency kit for her in case they got stuck out of the TARDIS for more than a day again. Maybe he could threaten them with a rather alarming shade of pink lipstick.

"Where's Ace's explosives when you need them?" the Doctor muttered, rummaging through the pockets. His pile of food was building quite nicely, but his pile of escape-worthy things was still empty, save for a pear and a banana peel, which were joined by orange rinds.

The door to his cell was suddenly thrown open and Dr. Everett stood in the doorway.

"I told you it would be useless to protect your companions. We found them."

"What?" the Doctor asked, worriedly. He pitied the poor soul whom they thought was connected to him.

A voice drifted down the corridor, protesting emphatically. "Get off me, you horrible – Ouch! That was my foot, you hulking ape!" It was familiar and wonderful and completely impossible.

The guards dragged a figure through the door and thrust her at the Doctor, who caught her in shock. Dr. Everett pulled the door shut, locking it, but neither of the prisoners noticed. They were too busy staring at each other.

"Jenny?" the Doctor whispered hoarsely. Jenny stared at him white-faced before flinging herself into his chest and embracing him in a vice-like grip. Her shoulders shook lightly as her tears soaked the Doctor's shirt. He couldn't have cared less. He pulled her to him, burying his face in her blonde hair and pressing kisses to the crown of her head. They stood for a few minutes in blessed silence, reveling in each other's presence.

After a few minutes, the Doctor pulled back to frame Jenny's face in his hands, his eyes raking over it while she gave a tremulous smile. "How?" he asked softly.

She shrugged. "I dunno. One minute I was dying and the next I was laying on the table in the theatre. Cline said there was this weird gaseous stuff coming out of my mouth before I woke up, like inside the terraforming device."

"Oh," the Doctor's eyes widened in realization. "Of course. It was revitalizing the entire planet. It just thought you were another thing to revive. That must have mixed with the Time Lord DNA, not enough for a full regeneration but just enough to tip the scales in your favor. Oh, that is brilliant." He grinned for a moment, before it slid off his face. "And I just left you there. I'm sorry. I'm so, so sorry." He stepped back quickly, not looking at her anymore.

Jenny stared at him, contemplating the twisting feeling in her gut. When she'd woken up and realized her father was no longer there, she'd felt betrayed. The least he could have done was stay for her funeral. But no, he'd just upped and left. Yes, he'd been in pain, and she understood that of course, but so had she. She had had the realization as to what kind of man her father really was. Oh he was wonderful, her hero, but now she knew why he ran. He ran from the pain, from all the reminders, from the guilt, and so, he'd run from her too.

And now he was standing in front of her, as though waiting for her verdict, the final blow.

She shook her head. "We can cross that bridge later." He looked at her sharply, understanding. It wasn't forgiveness but it wasn't rejection either. He allowed himself to hope.

"For now, though," Jenny said, turning. "We have a jail to break out of."

The Doctor warned her it was deadlock sealed, but she just grinned and said, "Well, you're a bit behind the times, old man." She reached into her pocket and pulled out a packet of –

"Chewing gum?" the Doctor asked quizzically. Jenny nodded, popping a piece into her mouth and chewing furiously. After a minute she pulled the gum out of her mouth, much to the Doctor's disgust and shoved it into the slight crack between the door and its frame. There was a sharp bursting noise and the door swung open silently. The deadlock seal had vanished and the lock was charred. The Doctor gaped in amazement, before looking at his own pile of foodstuffs accusatorily.

"Shall we?" Jenny asked, impishly gesturing to the empty corridor. The Doctor shoved everything back into his coat, pulled out his sonic and led the way out.

"So," he whispered conversationally. "What are you here for?"

"I crash landed. I was hoping someone could help me get parts and repair my ship. It's a total wreck. You?" she replied.

"Landed and had no idea where I was. Just decided to take a walk really. Anyway, ditched the gun, have you?" he asked, looking at her.

"Sort of," Jenny answered, pulling a gun from the back of her holster. The Doctor's eyes narrowed. "Don't worry, it's set to stun." He still didn't look convinced and Jenny huffed angrily. "Well, not all of us are nine hundred year old Time Lords who can save the world with the gift of gab. I'm only three remember? I had to learn to fend for myself," she tossed at him acidly.

He flinched and she almost felt bad. Almost.

"Where are we going?" she asked, changing the subject.

"Back to the TARDIS," he replied, looking around cautiously. "There's nothing alien here. Just human greed mixed with stupidity and the Shadow Proclamation can handle that. I'm not risking you here any longer. Come on."

Jenny was furious and hurt. Even as she followed him blindly, her mind was repeating his words over and over. Risk? Is that all he thought she was? A liability? He'd seemed so guilty before about leaving her behind, but she couldn't be sure. What if he never meant to take her away? What if she'd lived? Would he have just left her behind?

They approached the TARDIS with little incident. Finally feeling that they were out of harms way, they began to run. Almost immediately, gunshots rang out, followed by shouting. They ran faster, throwing themselves at the door while the Doctor fumbled with the Yale lock and key.

He thrust the doors open just as he heard Dr. Everett scream "No! You will not take this from me!" There was the sound of something winding up and firing with an electrical crackle. The TARDIS doors slammed shut.

"Safe!" the Doctor crowed in triumph. He turned to Jenny excitedly and his jaw dropped in horror. The little blonde was doubled over in pain, clutching her head and whimpering. "Jenny!" the Doctor dove forward to catch her as she fell, a horribly familiar scene playing in his head – one that he never wanted to repeat. "Jenny, Jenny what's wrong?"

"M-my head," she cried. "It hurts so much. Make it stop. Please, make it stop." Tears ran down her face.

The Doctor scanned her quickly, reading the results with a growing sense of despair and fury. "Memory disruption gun," he said grimly. "Illegal in the majority of the universe. She was probably aiming at me. Didn't want me to spoil her precious operation." He took Jenny's face in his hands, forcing her to stay in eye contact with him. Tears of pain were pouring down her face. "Jenny, it's twisting all your memories and you've only got a few years worth. You have to fight it, understand? Focus on my voice, come on! You can fight this." He scooped her up and ran to the med bay. Placing her gently on the bed he started hooking her up to the brain scanner, watching her brain waves in apprehension. They were fluctuating wildly, twisting and turning, warping.

Jenny let out another cry before looking at him sharply, her eyes red and puffy from crying and her cheeks stained with tear tracks.

"You left me," she whispered in a voice that just barely resembled her own. The Doctor froze, watching her cautiously. "You watched me die and you just left me there! Do you have any idea how scared I was?" She was screaming now.

"I'm sorry," the Doctor croaked, reaching a hand out for her, but Jenny flinched away. She jumped off the bed and doubled over clutching her head in pain.

"Dad, it hurts," she whimpered, her voice changing back, before she let out another cry. "Why didn't you want me? Was I just not good enough for you? I'm only an echo after all. Remember? Because I certainly do." Her tone was scathing. "All I wanted was to make you proud of me. I tried so hard. And for what?" She collapsed to the ground, her energy spent, shivering lightly as the rays continued to try and twist her memories.

The Doctor dropped to his knees and cradled her into his lap, ignoring her struggles. His heart was slowly breaking as he watched her fall apart, slowly cracking with every accusation thrown at him, like knives because they were just so, so true. He placed a gentle kiss on her head before murmuring softly.

"I wanted you, you brilliant girl. I'm so sorry I left. I was scared, Jenny. So scared of losing my family all over again. I don't think I would be able to survive it. I shouldn't have run, I know, but that's all I've ever known." He let out a bitter laugh. "Running my whole life from everything I never wanted to face – the Time Lords with their arrogant superiority, my family and their disappointment, every companion whose life I've ruined, and now you." He tightened his embrace. "I don't know if I can make it up to you, but I swear, I will do everything in my power to try. I promise, I love you. Do you understand?"

She made no motion and the Doctor realized she'd fallen asleep. He looked up at the monitor again. The fluctuation was slowly returning to normal, but there was still a risk. She needed help fast. Placing his fingers at her temples, he closed his eyes, diving into her mind.

He was standing in an open field. Jenny's mind was filled with warmth and innocence and although he had always known, the Doctor was struck at that moment with just how much of a child she still was. Her open curiosity and trust was like that of any toddler, willingly trying every new thing regardless of the dangers. Of course, there was still the soldier instinct that had been programmed into her by the machine, but it was softened, muted.

He strode forward calling her name loudly. The field seemed to stretch on forever and after a while, he stopped knowing it would be fruitless. He stood there thinking. Where would Jenny go if she felt threatened or scared? What was her "happy place" so to speak? Then it clicked and he closed his eyes, imagining his beautiful ship. After all, where does any little girl go when she is scared but her to her father?

Jenny was asleep, curled up against the aged wood. A venomous viper wound its way up her legs, slithering around her torso, slowly constricting its massive body. Jenny's breathing was becoming shallower and shallower but she made no effort to escape. The Doctor wrenched it off her with difficulty. She remained asleep. Her young mind, he realized, must have shut itself down in order to protect itself, not knowing any better. The viper, which was what the rays had been personified as, tried to attach itself to the Doctor but he flung it away. Without a mind to corrupt, the viper silently dissolved into harmless nothingness.

The Doctor knelt and tapped Jenny's face trying to wake her.

Jenny stirred, seeming bewildered. "Where am I?"

"In the med bay," the Doctor said, smiling. "Right now though, we're in your head."

Jenny reached a hand to her head, her mouth dropping in awe. "I can hear you, before you say anything."

You're safe now. The gun's influence is gone. Just sleep and recover alright? The Doctor added silently. Jenny nodded, resting her head once more against the TARDIS and drifting off to sleep.

The Doctor pulled out of her mind. Picking up his sleeping daughter, he walked out of the med bay. A new door was set into the wall right across from his bedroom. It was made of a deep red-hued wood and an elaborate cursive 'J', like a decorative one from old illuminated books, was inlaid in what looked like gold. It swung open to reveal a plain but comfortable room painted a light shade of lavender.

"Thanks old girl," the Doctor muttered, tucking Jenny into the bed. They would have plenty of time for talking later. For now, she would sleep.

The Doctor backed out of the room, heading for the console room. He hopped onto the jump seat and began sending a message to the Shadow Proclamation, forcefully hitting the keys with all the built up fury and frustration. With the message sent he sighed and slumped forward. Picking up his sonic screwdriver, he ducked beneath the console, distracting himself with some minor tinkering.

Nearly four hours passed and the Doctor didn't emerge, lost in his own world of mechanics and wires. The TARDIS sparked irritably a few times but finally settled, resigned to his incessant need to work. He didn't notice anything, until fuzzy-sock covered feet padded softly across the grating, stopping just in his line of sight.

He paused, and pulled himself out from under. Jenny was standing there, staring at the floor. She had wrapped herself in a huge fluffy robe and looked positively miniscule in it.

"Feel better?" the Doctor asked softly. Jenny nodded biting her lip. The Doctor waited.

Jenny teetered back and forth, before finally bursting out, "I didn't mean it! I'm sorry! "

"Yes you did," the Doctor said simply and she stepped back as though he'd slapped her, looking guilty, but he continued. "You had every right to mean it, but I'll keep my promise this time and try to make it up to you, any way I can." Jenny looked at him hopefully and he held out a hand to her. "I'm not leaving you ever again." She took it and he pulled her forward to look at the TARDIS monitor. "Where do you want to go?"

Jenny smiled tremulously. "Somewhere amazing."
"We'll probably end up having to save a planet and battle aliens," the Doctor warned.

"And there'll be an awful lot of running to do," Jenny finished. The Doctor beamed manically at her, flinging the TARDIS into the vortex at random. They would heal with time, and they had all the time in the universe.

A/N: Ok, I know Jenny seems like she overreacts in part of it, but I did that on purpose because toddlers tend to overreact about everything and emotionally she's still just a baby. I hope you liked it!