Have you ever wondered why in Generation 2 (Gold, Silver, and Crystal) that there is only one place in the whole of Johto and Kanto that you can breed Pokémon?
I can tell you why, but I warn you. You may not like what you hear, especially if you feel particularly attuned to the suffering of animals in our own world. With that out of the way I shall begin.
A lot of emphasis was put on Team Rocket's little science experiment at the Lake Of Rage and soon after that their takeover of the Radio tower. When all the while they had already set up a much larger, but more secretive operation. You see, the daycare man and his wife were not the first to discover that Pokémon laid eggs. This was first the discovery of a lowly Rocket Grunt who was in charge of looking after the captured Ditto.
The Rocket Grunt, Hiroshi, thought he had the easiest job in the whole organization. Not once had he run into that eleven-year-old child who had single-handedly defeated Team Rocket not even a year ago, and he was not respected enough to have his plans follow through, so he's never messed up so badly that he'd have to come face to face with Giovanni to explain himself. Hiroshi really did have it easy, all he had to do was make sure the Pokémon were not too loud, that they were generally fed and on the rare occasion that they soiled themselves, he had to wipe it up with a rag.
The Ditto were kept in squalor. Hiroshi was regularly required to electrocute them if they were not silent. However most nights they remained silent, with only a sad humming song that resonated down the filthy hallway. Each cage, no more than 20 cm x 20 cm, and electrified mesh wire held two Ditto; the transformation pits also held two Ditto but were 10 ft x 10 ft wide to accommodate for the shape shifting to larger Pokémon, all controlled by electrical frequencies as to what Pokémon they became. They all sang, one after another and as the song spread outwards Hiroshi felt his eyes begin to flutter.
He felt compassion for the beasts, cramped in their cages, or in the transformation pits. Besides, the song wasn't unpleasant to listen to, but falling asleep on guard duty was a sure-fire way for things to go wrong. To help keep him awake he reached for a Pokeball. When the energy was released from the ball, an Arcanine padded forwards toward its master.
"If you smell anything out of place, or if they try to escape, use whatever force you think necessary." The Arcanine nodded its large head and padded down to sit next to its master. With that, Hiroshi nodded his head and almost instantly fell asleep, the song continued to resonate in his dream. He felt he had not slept all of ten minutes before he was woken by a terrible squealing and panting. His eyes bolted open and in a panic. He scanned the battery cages and the transformation pits. The song had died and in its place was a horrible screeching noise, as if all of the Ditto began to panic at once. Hiroshi had only a split second to run to the lever and flip it down before several sparking volts seared through the wires, causing a high squeal from the confined Ditto before they knew to be silent once more. But still, the whimpering and hushed language continued between them as they shuddered in their cages.
The panting continued. Hiroshi stepped slowly along the isle, looking inside every single cage. The Ditto stared back at him with an expression of pure fear as they shook from cold and hunger. It was in the first transformation pit that he found his Arcanine, panting. Under him was one of the transformed Ditto, in a shape that Hiroshi did not recognize. It was dog shaped but was black with white horns from its head and a long whipping tail, the Ditto-dog panted helplessly while under the Arcanine, the searing pain of a forced transformation to an unfamiliar shape confused and distressed it. Arcanine gave a long, loud yelp before dismounting the Ditto-dog and padding back towards Hiroshi, jumping the fence with ease.
Hiroshi himself was still in shock as he watched the Pokémon shape in front of him, he had never seen anything like it before. The Ditto-shape looked sickly, many of the bones that would have been internal showed on the outside of the dog-like body, it panted again before collapsing. Hiroshi shook his head and ushered his Pokémon away, such strange things were not uncommon to see with the Transformation pit Dittos. Sometimes with the different currents, the Ditto changed shape into structures they had never seen before. Excited by the concept of new Pokémon, Team Rocket had tried desperately to get the Ditto to stabilize into their new forms to no avail. What disturbed Hiroshi however, was the way in which his Arcanine had simply mounted the poor creature.
In the weeks that followed, Hiroshi had taken care not to release any of his Pokémon from their balls while he was on Ditto duty. He paid extra attention to the dark dog ditto, who lay sprawled on the floor of the pit, tongue lolling from its mouth and its breathing extremely labored. A lack of food, water, and cleanliness made it look even worse than it had already. Hiroshi smirked a little. "You got the look of a doomed Hound," The dog-Ditto looked up to him and shakily stood on its four legs. What happened next astounded and scared Hiroshi for the rest of his days. The Ditto-dog scrunched up its face and howled in pain, causing the caged Ditto to again scream with terror. Hiroshi ran to get one of the pokédoctors, thinking that the Ditto was dying. Now that would be an offense to face Giovanni with.
When they both had returned, the Ditto-dog was still standing, and howling inhumanly, a high pitched squeal as its innards burst from its backside and fell into a bloody heap behind it, a large, solid mass among the offal debris. The doctor jumped into the pen immediately, but the Ditto-dog had already begun to dissolve, first into a pinkish gelatinous goop and then it began to shrink until it was nothing but liquid. The Ditto had expired, but still left on the dirt of the pit were the offal and the large mass.
The doctor sifted through the offal and picked up the mass, to his surprise it was steady in his hands, and held it up to Hiroshi. It was an egg.
The egg was monitored for days on end by the scientists and Hiroshi, who took a personal interest in his big discovery, until all at once, the news spread in the department that the egg was hatching. There was a big commotion at the department, as people crowded around the small table. The egg began to shake and crack, little splinters coming off in pieces before a dark head emerged.
It was disgusting, it was gruesome, it looked evil, it was new: A puppy, black as night with its skull seeming to be visible on the outside and its ribs protruding from its back. It was perfect. Hiroshi stepped forward, parting the crowd. His mind swimming with opportunities. If this Pokémon lived, thrived and reproduced then he had successfully achieved by accident what the scientists had been trying to do since the Dittos were captured. He had created a new Pokémon.
"Its mother, Ditto, was a doomed hound. Houndoom. This is our hound. Houndour." The scientists nodded silently in agreement, all astounded by the events which happened before them.
From that moment onwards Hiroshi was presented before Giovanni with the Houndour and was promptly put in charge of the Ditto evolution project. For the next two years, Hiroshi studied the Ditto in the pits, forcing them into strange and grotesque shapes with the aid of the electrical current, and then forcing them to breed with the male gender of a similar looking Pokémon. He managed to do this successfully with at least a hundred different variations of the Ditto. All of them managed to give birth to eggs. Some eggs never hatched, some eggs hatched and the Pokémon died within a few days, some eggs hatched but the offspring were infertile or never evolved, but there were many, where the eggs hatched and just like Houndour, managed to successfully evolve and re-breed.
After this was successful, they even tried it with Pokémon that they already knew. Pikachu-Dittos had strange mini-chu babies, Magmar-Dittos had even stranger mini-mar babies. The discovery was outstanding, but tragic as none of these offspring lived very long after the mother Ditto had expired. Which lead to the development of better medical care, and gradually the Ditto could sustain more than one offspring in their lifespan, but still the babies did not thrive.
This continued for many years until word of mouth began to travel, with wealthy Pokémon collectors sporting brand new types of Pokémon. The Ditto, their eggs, and their babies were all mysteriously released one night and Hiroshi was found dead in the labs, his body charred beyond recognition through visual means alone. Whether this was a revolt from the tortured ditto who just so happened to escape, or whether Pokémon activists managed to infiltrate and release the Pokémon themselves is unknown.
It was several years afterward when many of these new species had begun to thrive in the regions of Johto and Kanto that an old couple living just outside Goldrenrod came home to a rather shocking discovery. A large, soft egg, nestled between two Pokémon they were looking after.
Rocket continued the project however, with whatever Ditto they could find. Still to this day are they trying to manipulate them. And with a bigger gene pool than ever before, there is no end to the mutations they can force on those poor Battery Dittos.