This story will go over several chapters and contains much sex, homosexuality, cub sex, incest, impregnation, egg laying, rape; gore and much more (dunno what will come to my mind later :P) if you feel uncomfortable with it then don't read it.
For the sake of the story Pokémon are growing up faster than human (more like animals) but can get as old as humans can get. The aging process will be (but not exclusively):
Hatching-1 year baby/toddler
1-2 years child (can breed with a species depending chance of impregnation)
2-3 years teenager (sexually mature)
3+ years mature
In rare cases these ages might not be of matter because of special conditions or species (like legendaries) but it counts for the general population of Pokémon kind.

But now without further delay to the story. have fun.

The world was a dangerous place. The once so bright and great Pokémon society was at the brink of extinction. A virus had spread over the whole world and killed nearly the half of all Pokémon. But even the other half wasn't spared from it. All of the rest of the infected Pokémon changed. Before the virus all Pokémon were sentient and the technology and other things like art and entertainment flourished well. Now all Pokémon that were infected and didn't die became feral. They acted only on instincts. The few Pokémon that managed to not get infected made less than 0.01% of the whole Pokémon kind. Now the most Pokémon that were left were living in the barren cities centers trying to safe that little of civilisation that is left.
The low population made the guilds desperate and so they decided for a drastic step. To make sure that the civilized Pokémon kind wouldn't go extinct they started a repopulation program. That meant nothing more than that each guild opened a breeding center where guild members and other Pokémon were working to repopulate the world with sentient Pokémon. To make everything as efficient as possible they collected Pokémon that were as compatible as possible.
But of course that had also a downside. Some Pokémon became greedy and knowing that the guilds didn't have enough power anymore to handle many thieves and other criminals they created their own little illegal breeding centers where females and males were forced to breed. With other words they raped every male and female they got into their claws. Even a few of the guilds forced their members to breed even though they kept it on a low profile by seducing them with money and promises to sign contracts that made their members sex slaves but that was luckily rare and the other guilds often cut contacts with them.
Sam sighed as he looked out of the window as he thought about this and more. It was raining. He took on his coat and hat as well as his other rescuers equipment. The now a bit more than two years old Minun didn't like exploration in the rain. The sound of the rain was disturbing his hearing sense as well as it would wash away the smell of foes. 
Today they would have to work with other teams to catch a bandit group that caught every female rodent-like Pokémon they could to keep them as breeding stock. One female managed to flee while acting as if there was a problem with her pregnancy. She ran away as she was not watched and managed to get to a rescue team that brought her to the guild and told them everything.
The leaders quickly called in all teams and ordered to get ready immediately to catch the bandits before they would be able to flee with the victims.
Sam entered the kitchen and looked to his sister. "Are you ready?"
The female Plusle nodded. She was just some minutes older than him but was much smaller.
Sam nodded. "OK. Then let's go." He rushed out of the door of their dorm followed by Sammy his twin sister.
He noticed that the leaders had called for more than just the usual amount of teams. This must have been a big group if there were so many teams. Sam gritted his teeth. "Just great... This seems like a big one..."
Sammy nodded. "We should team up with one or two other teams just to be safe..."
Sam nodded. "You think you can handle it?"
Sammy nodded. "It will be fine..."
Sam looked to her for another second before nodding. His sister never was the social type. She had problems talking to others because she was so sickish in their childhood. Also the other kids always treated her like an outsider because of her high intelligence and her ability to remember really everything. While he was a genius in many areas and was pretty good in convincing others she was like a walking encyclopedia. After all she had spend the majority of her life with reading and since she just needed to look at a page to be able to remember it word for word she had read through the whole library within a half year.
"What do you think what Pokémon we will have to face?" Sammy looked to him nervous.
Sam shrugged. "The reports said something of mostly rodent like Pokémon. Their leader seems to be a Raichu. So be cautious."
Sammy nodded and shivered a bit.
Sam knew what his sister was thinking. She was about one and a quarter year old as she was on her way home from the library. Some thug that was a Raichu tried to bust a nut on her but she got saved by the guild leader. That was also the reason why they became guild members. But till today she feared the Pikachu line a bit because of that trauma.
As they finally reached the podeum Sam looked around. It must have been the half guild that had collected here.
"As you all know we got ears of the area where a bandit group is operating from. Sadly we don't know the exact position what will make everything harder but what we know is that the bandit group has roughly 30 members." The Riolu on the podeum said.
A murmur went through the croud. 30 members was bad. The guild only had about 90 operating teams and only the half of them were present. If they had to spread there was a good chance that the ones who would find them would have a rough time.
The Riolu looked at them till they were quiet again. "We will pair you in two group teams. Lower rank teams will get together in three team groups. If you find the bandit outpost don't attack. Send a signal so the others know where you are and wait for reinforcements. Only act if they try to flee and try to buy time. Don't risk your lives. If you are outnumbered or overwhelmed by strong enemies then flee. Let the stronger teams handle the bandits. The rookie teams only observe and don't fight at all. The only thing you do is when the fight has started you rush in and get as many females out as you can. Don't get in fights. We don't want to lose more members like last month."
Sam gritted his teeth. Last month they found a bandit camp that had only 10 members but the teams sent were spread too far over the area. The two teams that found the bandit camp were completely killed.
"Now get your butts out there." The Riolu jumped down from the podeum.
It was normal that the teams would form groups by themselves. The rookies were normally the ones who had to wait till other teams would speak to them or till all higher ranked teams were gone.
Sam and Sammy were of one of these rookie teams. They had to wait till only the rookie teams were left. Sam looked to Sammy. "Let me do the talk and just stay with me."
Sammy nodded and then suddenly squeaked nervously trying to hide behind her brother.
As Sam turned around to look what was going on he saw a male Pikachu and a female Plusle. He had to admit that the Plusle was pretty and that his instincts wanted to do something different now than going onto the search for bandits. He quickly pushed the thoughts aside and greeted the two. "Hello. How can I help you?"
The Pikachu grinned. "Well I thought we could go together." He looked to the Plusle. "Don't worry little one. I am not biting or anything."
Sam grinned. "Actually she is the older one of us. She is just not very fond of the 'chu line." He looked to his sister. "You think you could handle it?"
Sammy looked to the Pikachu nervously and nodded.
Sam smiled. "OK. Well then. I am Samuel but my friends just call me Sam. This is my older twin Samantha but you can call her Sammy. Please don't be offended if she won't speak to you."
The Pikachu smiled. "Oh... OK. That's fine. I hope you know that not everyone of my line is a bad one." He pointed with his thumb to his chest. "I am Kiiro and this." He signed with his hand to the female Plusle. "This is my younger sister Orenjii."
Sam smiled and nodded. He would have to watch out for this Pikachu. He was smart and instantly noticed that his sister's fear came from something that happened in her past and that one of the Pikachu line was involved in it.
Orenjii twitched her ears cutely as she waved her hand a bit shy towards the two. "Nice to meet you."
Sam smiled and bowed down. "It is nice to meet you too. Especially such a pretty lady like you."
Kiiro chuckled. "Wow. Just met her and already using your silver tongue. I already heard of you Samuel Spark. You seem to break a lot of girls hearts."
Orenjii blushed and looked to Sam nervous.
Sam smiled. "I am sorry if I break hearts. I was just raised to be nice to females."
Then Sam noticed something tugging on his coat. As he looked down he saw his sister pointing towards a group of three Pokémon. One was a male Growlithe, one a female Alolan Vulpix and one a male Pidgeotto.
Sam smiled. "Oh a good idea. How about we get some type coverage with that team?"
Kiiro looked over to the other team and nodded. "Yeah sounds fine to me."

About one hour later they were in the southern area of the barren city. It was a bit creepy with all the crumbling buildings that once were full of Pokémon. Even now most of them were inhabited by Pokémon but those were all ferals. Well except for the building that was probably used as base by the bandits.
The Growlithe growled. "I get a track. It leads further into the southern barrens..."
Sam nodded. "OK."
They went further south and soon they found themselves in the slums. It was the area that was inhabited by the poorest Pokémon before the virus happened and so the Pokémon build wildly wherever was space. There were no maps of that region and it was like a maze already before the virus. Now it was even worse because it had partially become a mystery dungeon what made it impossible to navigate in there.
"Damn... They are smart... The slums... there they will be nearly impossible to find if you don't know where..."
The Growlithe growled again. "I lost the track..."
Sam looked to him. "What?"
The Growlithe looked back to him. "It is like if it just disappeared..."
Sam looked around. "That should be impossible... There is no natural reason why the track disappeared except..." He looked around. "OK. Spread out. They must be around here somewhere. They must use some chemical to neutralize their scents."
Kiiro looked to him confused. "Why do you think that?"
Sam grinned. "Because if an exploration team comes through here and if the area reeks of sex then they would be busted. They probably used some chemical to get the scent of sex away. That's why there is no trace." He looked to everyone. "We will spread out. Be careful. If you see anything don't attack and give us a signal."
The others nodded and they spread out. Sam went into a building and looked around. The crumbling walls made it easier to navigate. He could basically go from one building into the next or out onto the streets again through holes in the walls.
After about an hour he went back. He hadn't found any trace.
As he was back Kiiro, the Growlithe and the Pidgeotto already waited. 
Kiiro was nervous. "Where are the females?"
Suddenly a feeling of doom crept into Sam. "Which direction did they go?"

Sam looked around. "No trace of them..."
Kiiro growled. "How could we be so dumb?"
Sam gritted his teeth. "It is my mistake... I was responsible for her..."
Kiiro looked to him. "What do you mean?"
Sam searched around for any track. "My father said that she only would be allowed to join the guild if I keep an eye on her..."
Kiiro shook his head. "You can't be responsible for your sister... Things happen..."
Sam growled. "But I was the one who convinced her to join the guild with me... She followed me even though she knew she would probably have to participate in the repopulation program... She only followed me because she trusted me and now this..."
Kiiro slapped him right across the face. "Damn it Sam. Stop thinking about this bullshit. You said you are smart. Now it is time to proof it. Where could they have gone?"
Sam looked to him for a moment. "I have no idea..." He looked down at his hands. "I have no fucking idea..." Then he froze. He saw what he missed out all the time. "The sewers..." He looked right at the sewer entrance under him. "Arceus damn it. They are in the sewers!" He looked at the Pidgeotto. "You stay here and send the signal. Inform the others where they can find us." He opened the sewers. "Kiiro, Bruno, you two come with me." He jumped down without a second thought.

Sammy squeaked as she was shoved into a cell together with Orenjii and Tira. She looked around nervously. There were several other females around them. The most of them were pregnant. The rest of them seemed too young and immature.
Tira looked to them. "Are you all OK?"
The most of them looked down but some nodded.
Tira smiled calmly. "We will get you out of here. Don't worry."
"As if you could keep that promise. Your guild partners don't even know where you are." The Raichu chuckled. 
Sammy squeaked nervously and tried to hide behind Tira.
The Raichu grinned. "Oh... A Plusle... I didn't have a Plusle in a while..." He opened the door and entered the cell. "Oh there are even two of you. I will have much fun today."
Orenjii squeaked nervous and tried to hide behind Tira as well.
"Let them alone!" Tira growled. "If you want someone then take me."
The Raichu chuckled. "Oh, thank you for the offer but I prefer some Plusle for today." He went to grab Sammy and Orenjii.
Tira hissed and charged at him using her Ice Shard at him but he easily blocked the attack.
He growled and grabbed her tossing her against the bars. "Hey guys. Who wants some fresh Alola-Vulpix? She needs some manners and some egg fillings." He chuckled evil as a houndour came in grinning widely. "Oh I am burning to fill some eggs into someone since morning. Time to get some cool down."
The Raichu rolled with his eyes. "Your jokes are terrible." Then he went over to Oranjii and Sammy grabbing them by their ears before dragging them off. "Oh, I will have some fun tonight."
The Houndour on his side didn't waste any time and just closed the cell door before he mounted Tira.
Sammy and Orenjii still could here her screams for help echoing through the tunnel as they were dragged away.

Sam growled and ran ahead. "Did you hear that?"
Bruno nodded. "That was Tira."
Kiiro ran faster following the Minun. "I don't want to think about what they are doing to them right now."
Sam nodded and then suddenly stopped. "Wait." As the other two stopped just behind him he was looking at a wall. He was staring at a strange sign. It was two straight lines crossed by a diagonal line. Sam growled. "Bruno follow Tira's voice. Kiiro come with me." He ran into the opposite direction of Tira's voice without another explanation.
Krio looked to the sign and then to Bruno before he followed Sam.
Bruno looked at the sign for a longer moment. "What does that mean?" Then he was taken out of his thoughts by another scream of Tira and ran to where her voice came from.

Sam ran around a corner. He glanced to the right and instantly saw the sign. two lines crossing making them look a bit like a tent. "Next turn left." He yelled back to Kiiro.
Kiiro seemed to have a bit problems to follow him. "H-How do you know that?"
Sam grinned grimly. "Sammy and I are twins. Twins often develop some sort of secret language. We did it through signs. We have so many signs we could write a book full with more than three hundred pages and yet we would have more signs. She used only the easiest to tell us the direction. I think they got separated from Tira." He rushed around the corner and used his momentum to punch the Pikachu that was waiting around the corner right into the guts knocking him out right away.
Kiiro gulped. "Remember me to never make you angry."
Sam twitched his ears. "You should wait till I find that scumbag that took my sister..." He stopped again. "There are five enemies ahead... one of them is an Emolga and three more Pikachu. One Pachirisu..."
Kiiro looked at him confused. "How do you-"
"Their steps. I have good ears. Do you think you can take the Emolga and one of the-" He was interrupted by a scream that chilled him to the bones and at the same time made his blood boil by anger.

Sammy was quick to act. She made many signs knowing that if Sam found them he would know what they mean. Luckily the Raichu didn't seem to watch her as he dragged her and Orenjii along. But as they reached some kind of hut built into the sewers she knew they reached the end of the line. Here it would happen and she feared every bit of it. She shivered so hard by the pure thought of it that she wasn't able to move or make any complain as the Raichu opened the door and threw the two Plusles onto a king sized bed. She would never know how they managed to get such a big bed down here without it rotting by all the fluids of the sewers but that wasn't important anyways. She only had one thought and that evolved around the statue of the huge Raichu standing in front of them blocking the only exit with his body. She needed to flee.
The Raichu grinned and looked from one of the two females to the other while taking off his gear.
Sammy looked at the gear. If she just could get a knife or something from the gear she would- Her thoughts were interrupted as he had pulled down his pants revealing his cock. It was huge and throbbed. 
He chuckled and locked the door. "Oh I will have a lot of fun with you two." He slowly went closer to the two. "Who of you wanna be the first to receive my eggs?"
Then something happened that threw Sammy totally off balance.
Orenjii hugged her crying and whimpering. "P-Please not..."
Sammy noticed that the other female Plusle was just as afraid as herself if not even more. Orenjii was younger after all and Sammy already had prepared herself to breed sooner or later. The notification that she would come into the breeding program already arrived her and her brother but Orenjii would probably be spared for another half year. She was still so young and something in Sammy wanted to protect the other Plusle. "Take me first..." She couldn't believe that she said these words herself but it was true. She turned to Orenjii. "Don't worry. Sam and the others will arrive soon..." She whispered to Orenjii.
The Raichu chuckled. "Oh! You are brave. But I will make you scream and cry too." He grabbed Sammy by her ears and pinned her down on her belly mounting her back trying to line his huge cock with her much smaller pussy. "You will carry a lot eggs. I can feel it."
Orenjii whimpered. "Sammy... Why?"
Sammy smiled to her but then the smile disappeared and a face of pain appeared. She screamed from the top of her lungs as the Raichu mercilessly plunged into her just caring for his own fun and pleasure and not caring for how painful the rapid speed of his thrusts into her felt for her.

Kiiro wasn't able to stop Sam. It looked to him like if the Minun was flying instead of running.
Sam screamed in anger as response of the scream of his sister. He just flew by the five bandits that just looked confused at the yellowish-bluish blur that passed them before they realized that two of them just lost their heads. Sam showed no mercy anymore. He was blind in rage and everything that would stand between him and the freedom of his sister would pay a high price. Kiiro tried to follow him but was soon facing the remaining three enemies. Two of the Pikachus were dead and the Emolga had a pretty deep cut in the arm probably loosing it. Kiiro acted fast and before they could react to the dead Pikachus and the blur that had killed them he knocked the Pachirisu out and was already attacking the remaining Pikachu. Only then they realized what had happened and that there was another foe for them but it was too late. Kiiro got the Pikachu knocked out pretty fast and with the at least broken arm the Emolga was no match for him.
Sam on his side had no other bandit on his path. The hut was just around two more corners and he didn't waste any time braking the door into pieces. Just as he bursted through the now broken door he had to see how the Raichu on top of his sister made one deep hard thrust and Sam knew that he just came too late or better said the Raichu just came in the moment. 
Sammy whimpered and looked to her brother. "S-Sam..." Her voice was weak and quiet.
That sent Sam over the edge and he rushed at the Raichu with a speed that was close to teleportation. The first two hits with his Trump Card move chopped of the Rauchu's arms and before he could react the Minun grabbed the Raichu by the throat and flung him against the wall of the hut.
The wall wasn't able to withstand the Raichu and gave in. The Raichu let out a scream of pain but it was short lived as Sam flung himself into the Raichu's back.
Even Sammy and Orenjii could hear the loud sound of the breaking spine.
Sam growled and piked the Raichu up by his throat again. "You filthy piece of shit dared to do that to my sister? You deserve more than this but knowing that you would be executed anyways I don't wanna let them take me the pleasure to do it myself." He was slowly choking the Raichu. "I wish I could let you suffer for much much longer than this but sadly this is all the time I have for you now. Enjoy it. It will be the last time I will waste any thought on you. You will soon be vanished from this world. You better pray that Arceus has more mercy for you than I have or your afterlife will be the worst nightmare."
The Raichu was already dead. He limbly hung from Sam's hand only his feet on the ground.
That was the moment when Orenjii noticed how big Sam actually was. But even though he was so much bigger than her and even though he just showed no mercy killing the Raichu in such a cruel way she had no other thought than that she admired him. The Minun who wouldn't hesitate to protect the ones he loved no matter what he had to do for it... The Minun that just saved her...
Sam just let the Raichu fall to the side into the mud of the sewers. He went back to the hut and wiped his hands clean on his coat before he took the two blankets of the bed and wrapped both Plusle's into them. 
Orenjii didn't even struggle. She just stared at him. She was hesitant but she knew one thing. She admired him and maybe even more. The softness with that he picked both of them up and carried them out of the hut made her feel save but her heart was pounding. She knew that she just fell in love for him. For his strength, for his kindliness, for his tenderness and for his will to protect those close to him. She couldn't resist and cuddled onto him.
Sam looked ahead. His face was emotionless. "Don't worry... Everything will be fine again..."