"Okay, okay. Let's all just take a deep breath and relax. I think I made you a bit nervous so you jumped the gun a little, " said Alan. "I usually like to draw out my stories and kind of build up the tension, but in this case I think I need to give away the ending to calm your fears."
Here is how the story was intended to play out:
Chapter 1 - Origin of the Rat Queen:
Mary (I'll change her name if it is a really big deal, but there are people in the real world that share the same name. Considering she is a giant rat, I don't anticipate a lot of confusion. But whatever, I'm flexible) is a sewer worker. During the outbreak, Mary and a coworker Brad were sent to check on a problem with the water. Brad is the macho type, annoying Mary. He taunts her with wild tales of sewer monsters. Mary thinks he is a blow hard, just trying to show off. But a rat uplifted with the Animalian virus that contaminated the water supply attacks and rapes Mary. Brad runs off like a coward, showing his true colors. Mary is converted during her assault. After the rat is finished, he apologizes. But Mary kills the Rat-man in a rage as retribution for what she considers a brutal attack. Weakened by the attack, Mary crawls to a dark corner to recuperate. She spends most of the time sleeping, emerging only rarely to eat. Later, she discovers she is pregnant. A government clean-up team enters the sewer to contain and clean up the virus. Mary misinterprets their claims of 'neutralizing the threat'. Thinking that that neutralize means 'kill', Mary scurries into a dark corner and hides until they leave. Later, she gives birth and cares for her young, feeling compassion for the helpless creatures. In time, her children have children and soon she is a grandmother. Very quickly she finds herself outnumbered. She is forced to adopt the fake 'Queen Mary' persona to maintain some kind of order. By the time word of Animalia reaches her, she is trapped in a world of her own creation. She fears her children would mutiny if she tried to leave. But she doesn't want to join Animalia anyway. She has heard rumors of Dr. Green's proposed 'cure' and wants to become human again.
Side note: Jeremy recognizes that a cure or reversion is impossible. He said so himself in the "Lair of the Rat Queen" chapter. He had hoped to curb some of his sister's animal features by selectively silencing certain genes, but has gradually come to realize that it is impossible (can't unscramble an egg). Of course, Mary doesn't understand this. I am not sure if you have caught on yet, but she has been driven insane by her isolation and living conditions.
Chapter 2: We should have snakes for a job like this (The rescue):
Chel aids a swat team consisting of wolves in apprehending the rats. Chel scouts ahead, swimming undetected underwater. Then reports the position of the lookouts to the wolves who peacefully take them out.
"Two up ahead. One on the shore, one of the ledge, " said Chel.
"Rats. We should have snakes for a job like this," said Shelly.
"Nah," said Hans, her wolf partner. "We can do this. Piece of cake."
"Just remember - we want them alive. Nothing lethal. They are just confused and misguided," said Shelly.
The swat team will rescue Jeremy (uninfected) and capture Mary. At no point did I intend for anyone to get infected with the rat version of the Animalian virus. The precious main characters would remain safe and unmolested. But in order to build a little drama, you have to at least present the threat. Heather and Jeremy would grow closer, each fearing the loss of another. Jeremy would abandon his attempt to cure, realizing it was a lost cause, a white whale chased by a madman. The attack would make him consider possibly converting a little earlier, afraid it might be forced upon him.
Chapter 3 - Not everyone can be saved
Jeremy visits Mary in her cell. She is in a large padded room with a single glass wall to allow visitors to view her. She has repeatedly torn up each mattress given to her to make a nest, so they simply stopped giving them to her. Mary asks Jeremy if he changed his mind about joining her 'kingdom', obscenely offering her breast to him and squirting milk on the window. Jeremy rejects her offer, reminding her that it won't work - she has been vaccinated. He asks her to reconsider joining Animalia. She refuses, again asking to be cured. Jeremy tries to explain that it is simply not possible. She brushes off what she considers excuses and asks why he is really here. Jeremy asks for her help. Her children have been successfully integrated into Animalian Society thanks to the educational programs. But there are still a small number of them hiding in the sewers. He asks for her help in getting them to come out and join Animalia.
"Oh, got a little rat problem, huh? Sounds like you need an exterminator," said Mary.
Mary refuses to help, telling him to come back when he has the cure. But not before warning him about how quickly rats can breed and spread, even to adjacent towns. Jeremy passes by Dr. Jones on the way out. Dr. Jones has been attempting to work with Mary, but has made little progress.
"Not everyone can be saved. Especially if they don't want to be helped. But that doesn't mean I won't stop trying, " said Dr. Jones.
Outside, Jeremy meets with Heather for lunch. She still wants to hurt Mary, can't stand to be around her. Jeremy reminds Heather of her own checkered past. They head off together, holding hands and discussing plans for the future.
End of kidnapping arc
"And that is the short version of the story. The chapters will be a bit more detailed and fleshed out, but I think you get the general idea. Just a quick side note - I don't really consider the 'rat kingdom' a cliché. I thought it was a pretty clever twist to have the 'kingdom' actually just be a con to help Mary keep her ignorant but more numerous children under control. It is really not a true 'Secret Society' because they don't induct new members or have any secret rituals. A better analogy might be some kind of family hierarchy or a feudal society. It is important to remember that Mary doesn't really believe in the society she has established - she doesn't really think she is a Queen, but needs the other to believe she is one to keep her power over them. But, I guess one man's cliché is another man's clever twist. Que sera, sera, and all that."
"I plan to add the next chapter as a branch of the "Halloween Terror: In the Lair of the Rat Queen!" chapter. It will keep readers from knowing the proposed ending in advance. You can chose to follow it or ignore it at your discretion. Again, thank you for your time."