AN: This story involves the 11th Doctor and Clara and comes after "The Zygon Inversion," though that doesn't really matter. To be completely honest, this story is just a fun idea I had and it doesn't make much sense; I'm not even going to try to explain how the Borg are in the same world as the Doctor. Just accept it and enjoy.

Resistance is Most Definitely Not Futile

"We need to get back to the TARDIS. Now," the Doctor said with great urgency.

"What are those things?" asked Clara, standing nearly frozen as she watched the men — if they could be called men — work in front of her. They certainly paid her no attention.

"They're trouble," said the Doctor, taking Clara's arm to pull her away. "We're in extreme danger right now. Level mauve."

"But they're just ignoring us," said Clara, trailing off as the Doctor began to drag her back to where they had left the TARDIS.

The Doctor and Clara Oswald were on Goolet III, a planet with a high level of technology and some truly fantastic theme parks. They were taking a well-deserved holiday. Especially after stopping a Zygon invasion … again.

Without warning the Doctor pushed Clara into an alcove, shielding her as two of the men marched past. "Are they related to the Cybermen?" Clara asked.

"No," said the Doctor, looking both ways before beginning to run again. "They're worse," he said cryptically.

After a few more close calls with the men — though Clara did not think the men would hurt them even if they saw them as they seemed to be driven to complete whatever tasks they were doing — they reached the TARDIS

But the door wouldn't open.

"What's wrong with your key," asked Clara, looking around furtively, picking up on some of the Doctor's nervous energy.

"There's nothing wrong with my key," said the Doctor absent-mindedly as he continued to fiddle with the door. After what seemed like a very long time, he finally got the door open and ushered Clara inside.

There was something very wrong with the TARDIS. Even Clara could see that. The usually bright lights were dimmed to an almost subterranean-looking glow of greens and reds. It was hot, much hotter than usual in the TARDIS. Clara found herself removing her jacket in an effort to cool her suddenly heated skin. Most alarming, however, was that the TARDIS' consoles had been removed, revealing wire and the TARDIS' living tissue beneath. Someone or something had been in here messing around with the TARDIS' electrical system. There were wires hanging out and devices affixed to them that looked decidedly un-Gallifreyan.

The Doctor had rushed forward and was peering into the TARDIS' operating system, trying to determine what exactly had been done. But he was showing much more restraint than usual and he was refraining from actually touching any of the jerry-rigged work.

Clara let out a startled shriek as one of the mechanical men wandered into the TARDIS' control room from a side corridor. She pressed her hand to her mouth, determined not to make another sound, and froze. But it didn't matter. She was nothing to the intruder. He ignored her and the Doctor and went to rewire something in one of the control panels. He was standing just next to the Doctor, but he never once looked at the Timelord nor gave any sign that he knew they were there.

As the man was absorbed in his work, the Doctor walked over to Clara, took her hand, and led her down a corridor and into a room she had never seen before. This room too was too hot and too dark. The Doctor tsked to himself when the door closed, knowing that he had not been looking for this room. The Borg had clearly messed with the TARDIS' operating system to an extreme degree.

"What are those things?" asked Clara, fighting to keep the fear out of her voice. She was used to seeing frightening things with the Doctor, but there was something different. These weren't just aliens. These were mechanized men who looked so human and yet so alien. These were advanced beings that had infiltrated the TARDIS, one of her safe places, and had corrupted it. And worst of all, the Doctor had done nothing. The Doctor seemed frightened too. To Clara, that was unforgivable. The Doctor was her rock when they came across the weird. While his own personal demons certainly haunted him, he never let the outer ones affect him like this. It only increased Clara's fear.

"They're the Borg," the Doctor said, pacing the small room.

"And what does that mean?" asked Clara, trying to keep the quaver out of her voice.

"The Borg is a Collective. They have a hive mind and work together as a colony to achieve their goal."

"What's their goal?" asked Clara, feeling her throat suddenly become very dry.

"To assimilate. Everything." Instead of asking more questions, Clara remained silent. She knew that the Doctor would keep talking. He always did. He was a plain old chatty Kathy, especially when he was nervous. "They used to be men, some human, some other species. But then the Borg came. When the Borg come, nothing remains. And they don't just destroy civilizations, they contaminate them. They absorb them. The Borg are driven to assimilate the whole galaxy. They steal technology and incorporate it into their own. They 'upgrade' the men they capture. They strip away everything that makes you you. In that way, you were right, they are like the Cybermen."

"So, how do we fight them?" asked Clara.

"I don't know," said the Doctor. "'Resistance is futile.'"

"How can you say that?" raged Clara. It wasn't like the Doctor to say something so hopeless and it made her angry. "Maybe they aren't interested in us. They let us go before."

"The Borg don't assimilate individuals; they assimilate civilizations," the Doctor said, recalling a conversation he had had with a good friend a long time ago. "As long as we don't get in their way, they'll leave us alone. But the minute we give them a reason to notice us, we're dead … or worse, assimilated."

"So you're just giving up?" snapped Clara. "You? The man who does the impossible? Who goes from world to world putting things rights? No matter the odds?"

"I'm not giving up," said the Doctor with a sigh. "I'm being a realist."

"You're being a coward," said Clara. "You have given up. You're just letting them assimilate you."

"No. I'm not," said the Doctor, not liking her tone. He liked being adored; he hated it when his companions saw his weaknesses.

"Don't you see? They are already winning. They are already assimilating you," Clara said quietly. "They haven't even touched you, and yet they are stripping away your identity. You're the Doctor. You don't hide. You fight back. You're clever and you outsmart your enemies.

"But they've taken that from you."

The Doctor just looked at her. He was out of options. Out of ideas, a stunningly unusual position in which to find himself. He always had ideas. But not now.

Clara gave him one more stern look before slipping back into the corridor. If the Doctor was not going to do something, then it was up to her. She didn't have a plan, but she had spirit.

Unfortunately, when dealing with the Borg, it really is best to have a plan. It was not long before she was captured.

Meanwhile, the Doctor was sitting in a room aboard the TARDIS that he used to know. But now he felt adrift. He and the TARDIS had been together for a long time, ever since escaping Gallifrey. All the self-reproach and self-recrimination was rearing its ugly head. He owed it to the TARDIS to help her; she was essentially his family. As was Clara. He needed to go find her and help her.

But he was scared.

He had seen what the Borg were capable of. He knew how dark this could — would — get. And he was afraid of what he might do. He struggled every day to keep the darkness at bay. He strove not to be a warrior, to remain a traveler, a doctor. But it was difficult to remain a pacifist when faced with such evil.

But Clara needed him. She had always come through for him and he would not let her down now. Pushing himself up, he entered the corridor, bracing for a fight. But none came. The corridor was empty. As he rushed through the TARDIS, he formulated a plan. His mind worked unlike anyone else's. The synapses fired more quickly, formed more connections. As he thought, he saw possible actions and their possible outcomes. He was able to weigh the pros and cons. He could do complex mathematical equations. He could see the connections that others couldn't. All this in a single moment.

But all thought stopped when he reached the control room. There were three Borg there. Someone who had once been a human male, a one-time Sister of Karn and his Clara. His Clara. But she wasn't his anymore. She had fewer modifications than her new companions, but it was clear that she was one of them now. Her skin was impossibly white, her hair covered in a cap, a new all-purpose arm with a cornucopia of tools and an infrared eye. And those were just the physical changes.

Her eyes bespoke of a greater and more sinister change. Her eyes, usually so warm, were now empty as she continued to convert the TARDIS.

"Oh, Clara," said the Doctor softly, mourning her and yet refusing to give up on her. He knew he wouldn't win in a physical altercation. The Borg were strong and adaptive. His screwdriver was not a weapon; he was outmatched. But that didn't mean he couldn't use their strengths against them.

So he retreated. And he worked.

He pushed all doubt aside.

He couldn't let this happen to Clara. He had to save her before the assimilation became irreversible.

He shouldn't have let her go off on her own. He should have stayed with her.

But he didn't have time to think about the coulds and shoulds. He needed to focus on the present. So he locked himself in one of the TARDIS' rooms — a room that had no real function and therefore would not be needed by the Borg — and he worked.

After nearly a full day of work he was done. He was ready.

He just hoped he was right.

Re-entering the control room, the Doctor was pleased to see that Borg-Clara was still there. He wanted to keep track of her. Unfortunately, so were the other two. It would make his job more difficult, but not impossible.

Whistling a jaunty tune that he didn't really feel, the Doctor approached one of the consoles and ripped out a wire. Immediately, acting as one, the three Borg in the room turned to him and began to advance.

Though the Doctor held up his hands in a sign of surrender, they kept coming. When they got close enough, the Doctor pulled a lever that sent a shudder through the TARDIS. The first two Borg were knocked down by the harsh jerks and unable to regain their feet; every time they tried to stand, they were jolted back to the ground. But not Borg-Clara. She was used to the TARDIS. She remained standing.

Just as the Doctor had hoped.

She advanced alone.

"Resistance is futile," she told him with a mechanical voice that sounded enough like her own true voice to sound so wrong to the Doctor. "You will be assimilated."

"Will I?" he asked jovially. "Then why haven't I been already? We've met before."

"We are Borg. We do not know you."

"Sure you do," said the Doctor. "Dig deep into those archived Collective records. Go to the planet Trifflo; I was there. One of your Cubes blew up. That was me. That was during my angry phase. After all, I had killed all of my people; why not kill all of yours?"

"The Trifflo destruction resulted from a cascade failure. Not one man."

"Are you sure about that?" asked the Doctor, drawing Borg-Clara in. While she no longer had curiosity, the Collective would want to know what he did and how he did it to prevent further errors.

"You will tell us what you did at Trifflo," said Borg-Clara, now within arm's reach of the Doctor.

"Why?" asked the Doctor.

"You will be assimilated. You will tell us then."

"No, I won't," said the Doctor, lunging forward and attaching the device he had spent the better part of a day creating to Borg-Clara's eyepiece. First the device sent out an electromagnetic pulse — one with just enough innovation that the Borg were not resistant. Borg-Clara went down. Unfortunately, so did the TARDIS, her lights going off. Like the TARDIS, the Borg would be alright. After all, both were part organic, part machine. Hopefully, the second part of his plan would work before the Borg could effect a complete reboot of their system.

He saw Borg-Clara's eyes begin to flutter and he grew nervous. He hoped the computer virus he had introduced to her eyepiece would fry her implants but leave the woman intact. He hoped it would spread to the others.

Borg-Clara began to convulse. The other two did as well. The Doctor hoped his plan was working, but he wasn't sure. The TARDIS began to shudder again. Hopefully the virus would only target the Borg technology interwoven with the TARDIS and not actually damage the old girl.

After a short time, the shaking — from all four — stopped. The Doctor checked Borg-Clara and made sure she was still breathing. Her pulse was a bit thready, but there was nothing he could do now except wait.

He had never been good at waiting. He hated it. Think of all the things you could have done instead while you just sat and waited.

But to do something else would have meant taking his eyes off Borg-Clara, and he did not want to do that. He stared at her, as if the power of his gaze could heal her.

After what seemed like an eternity, she lifted her head and said, "Doctor, we hurt."

The Doctor's two hearts skipped a beat each. He had failed.

"No," she said, shaking her head. "I hurt. My head is pounding."

"Clara!" screamed the Doctor, grabbing her. "You're you."

"I'm me," she confirmed, looking rather green now instead of white. "Thanks to you."

"Doctor," said the Sister of Karn, "what did you do to us?"

"I introduced a malevolent computer virus," said the Doctor, relishing in his own brilliance. "It targeted only Borg technology."

"You saved us all," said the Sister.

"No," corrected the Doctor, sobering. "Not all of you. Only the Borg on this planet and in orbit. The moment you left the Collective, it would have shut off its connection to this area. You're a free agent again, but the rest aren't."

After taking a moment of silence for those who will likely remain Borg for the rest of their lives — if you can call them that — the Sister told the Doctor. "The Sisterhood of Karn will not forget what you have done here today. Ohila will not forget. I will not forget."

With that, she collected the man who had formerly been Borg and helped him out of the TARDIS. He appeared to be in shock and seemed willing to be led around. He had spent so long not thinking for himself — it would take time.

The Doctor turned to Clara, glad to see the life back in her eyes, though her eyes seemed shadowed and in pain. "Are you alright?" he asked, knowing she wasn't. He knew that face. He could see every line of pain and fear and doubt on her face.

"I don't know," said Clara. "I wasn't myself. I was still in there, but just barely. I felt shackled. I saw you and wanted to run to you, to help you, but we just kept walking toward you, and I knew that when we reached you, we'd assimilate you." She blinked rapidly, to keep the tears from falling. She had felt hijacked. It reminded her of watching Bonnie do things with her appearance. But this was worse. The collective hadn't just been controlling her body; it had been controlling her mind. She felt her mind being pushed down. She felt her thoughts changing. She would never tell the Doctor but, for a moment near the end, she had wanted the Borg to assimilate him, to destroy him. She had seen it as necessary.

The Doctor knew it could be dangerous to be left alone with your thoughts for too long. He needed to move around and actually do something. He stood and offered his hand to Clara, pulling her up as well. "I think it's time we removed those implants," he said.

"Please," she said, all of the pain and frustration from this recent experience coming out in the single word. She followed him into the recesses of the ship, now back to its normal glow and pleasant temperature.