A/N: This idea comes from some of the inscription on the Pandorica, describing the Doctor as the most feared being in the universe. Although that was meant for the Eleventh Doctor, I like writing the Tenth Doctor better. They're the same person in the end.
"Remember when I brought that dodo bird to life, Perry the Platypus?" Dr. Doofenshmirtz asked the blue agent who sat next to him in a metal cage. Perry rolled his eyes as he recalled one of Doofenshmirtz's more pitiful attempts to take over the Tri-State Area.
"Well, since then, I've been thinking of a better plan. Instead of reviving a stupid, powerless bird, I've decided to summon a minion that will be able to take over the TRI-STATE AREA!" He continued, dramatic music emphasizing the last words. "Behold! The Summon-Minion-inator! This Inator will scan all of time and space for the most feared creature and bring it here. Together, we will rule the TRI-STATE AREA!" Doof said, lifting his arms dramatically.
Perry, being unable to speak English, could not point out the major flaw in the mad scientist's plan- whatever was summoned by the Inator was unlikely to help Dr. Doofenshmirtz. After all, if you were so dangerous, why listen to a rather silly and irrational human? Still, if such a dangerous being was summoned, it was likely to destroy/take over the Tri-State area, maybe even the world. Perry was not afraid of Doofenshmirtz; he had always managed to stop him in time, and by now they were something almost like friends. However, he was afraid of what the consequences of this plot might be, should the man unleash a terrible monster. But try as he might, Perry could not get out his cage. Doofenshmirtz, for once, had made a cage that he could not get out of. The platypus would just have to wait for an opportunity to escape. In the meantime, he hoped that Doofenshmirtz would not do anything too stupid.
Perry tensely watched as Doofenshmirtz, cackling madly, pushed a big purple button which sat right next to another large, red one which was tantalizingly labeled 'self-destruct.' A red, radar-like beam shot out of the other end of the Summon-Minion-inator. The red light moved wildly around, scanning every direction of space- above, below, and even through the platypus and his nemesis, before finally vanishing.
There was a moment of stillness, then wind started blowing outwards from a spot close to the Inator. A wheezing sound that was somewhere between mechanical and organic, somehow managing to be both horrendous and beautiful at the same time, filled the room. Doofenshmirtz frowned. He didn't think his Inator was supposed to make that noise. A big, blue box materialized, pulsing a little more into existence with each whoosh.
"Well, that's anticlimactic. I summon the most feared thing in all of creation, and a 1960's police box appears. Perry the Platypus, did you know that police boxes were used in Europe to store criminals until help arrived? Maybe the most feared being is a dangerous criminal from the 1960s!"
Perry raised a skeptical eyebrow. Doof's ramblings were cut off as the doors flew open. A man with brown hair that's wildness rivaled Doofenshmirtz's own stepped out, quickly closing the doors behind him.
"Were you the one who rerouted the TARDIS's flight course?" the man asked in a British accent, directing a sharp gaze towards the scientist.
"Uhh... yeah, I guess. You know, you don't seem like the most feared being in the entire universe," he said in his whiny, scratch voice.
"I- What? What do you mean, 'the most feared being'..." The British man paused as he appeared to reconsider Doofenshmirtz's words and he paled, "Why did you bring me here? How do you even have the technology? It's only the 21st century."
"Erm, well," Doofenshmirtz sheepishly scratched the back of his head. "I wanted a minion to help me take over the Tri-state area. So I built the Summon-Minion-inator," he gestured to the device, "to find and summon the most powerful being in all of time and space. I expected someone more... impressive."
The man ignored the last sentence and gave Dr. Doofenshmirtz a very serious, stern, almost relieved and slightly exasperated look. "Why?! There are so many things that could go wrong with that plan! What if you brought a Dalek?! Just one of those could destroy the entire planet! That was incredibly stupid and dangerous!" After that burst of frustration, he calmed down. His voice was soft, and it trembled a bit with horror and troubled uncertainty. "So why did it bring me?"
"What's a Dalek?" Doofenshmirtz asked, oblivious to the Doctor's internal turmoil. "Also, who are you? Are you a criminal from the 1960's?"
"What? No!" His distraught mood appeared to evaporate in an instant. He turned towards the blue box, "She's not actually a police box. That's my ship. I'm the Doctor."
"How is that a ship? Doctor who?"
"Just the Doctor," he replied, grinning a bit for no apparent reason. "What's the platypus doing in a cage made of cheese graters?"
"I already went through the flashback explaining that," Doofenshmirtz said, mildly annoyed. "His name is Agent Perry. He's my nemesis. See! He's still wearing his fedora this time!"
The Doctor glanced back at the platypus, then looked back at Doofenshmirtz a little oddly. The mad scientist continued.
"I'm still not impressed by you. Shouldn't you be a bit more, I dunno, terrifying? How are you going to help me rule the Tri-State Area?" Doofenshmirtz instantly knew that was the wrong thing to say. The Doctor gave him a cold, sharp look, like the fangs of a saber-tooth tiger. (Although, since they were mammals, wouldn't its body temperature keep the teeth warm? Maybe if it was a really cold day, and the saber-tooth tiger kept it's mouth open. And how sharp were the fangs really? I need to come up with a better analogy. Oh! That's what I should've brought back to life, not a stupid dodo bird, Doofenshmirtz rambled in the back of his mind.)
"I'm not going to help you take over the Tri-State Area. Do you want to know why I'm feared by so many people? It's because I stop those who try to hurt or kill others, those who commit terrible crimes for power or money." He said, somehow simultaneously deathly calm and ferocious.
Perry the Platypus chittered in disagreement. The Doctor glanced over to him and continued, the edge of his voice, slightly softened, though it still was formidable. "I haven't seen you actually do anything that deserves punishment, but believe me, I will make sure that you never do. And I will not help you rule anywhere."
Doofenshmirtz nodded, quite a bit more than a little cowed. The Doctor strode over to Perry's cage and pulled out a strange metallic device from the inside of his suit. With a buzzing noise, the tip glowed blue and the cheese-grater prison fell apart.
The secret agent immediately launched himself at the Summon-Minion-inator, his webbed, yellow foot hitting the self-destruct button. The machine promptly exploded. The platypus tipped his fedora at the Doctor and jumped out of the window. A orange parachute with his face on it burst out of nowhere.
"Curse you Perry the Platypus!" Doofenshmirtz shouted. "And I just fixed that window too."
The Doctor blinked, his eyes curious and excited. "He really was a secret agent."
"I told you." The scientist sighed. "I'm just gonna go and order a new window. Maybe plan tomorrows scheme out. You can show your self out. Just don't break any windows. Or walls. Do you know how many times I've had to have the walls rebuilt?"
"Right then." The Doctor, for once, seemed uncertain as to what to say. "Don't summon me again." With that parting, he stepped into his blue police box. This time Doofenshmirtz caught a glimpse of something far bigger than one would expect to be capable of fitting inside such a relatively small space. It vanished, fading out of view, much like how it arrived in the first place.
Heinz Doofenshmirtz sighed. He had a window to fix, a scheme to plan and an Inator to create. Next time he would come up with something that didn't involve terrifying British men in 1960's police boxes.