While Amy's changes had shown up instantly, her son did not seem to have had any changes at the hands of the pod at the time its vapor first released. Though they could not have known, this was because he was prepubescent, and it had no affect on infants.
However, once the boy hit puberty, it first started to make itself known. One day, Timmy had had to run to the bathroom during dinner needing to pee. But when he tried, blood came from his penis. He freaked out, and had to embarrassedly tell his parents what had happened; they were also concerned, and took him and a sample of the blood to a doctor. After studying a little, they came to a strange diagnosis: it was mensural blood. They explained that sometimes people are born looking like boys but with ovaries instead of testicles, but noted that it was strange that Timmy was able to ovulate, since usually they would expect his ovaries not to function.
Everyone assumed that Timmy was just previously undiagnosed as having a female reproductive system, but then after more research of his medical history they found that until fairly shortly before the incident, he had had testicles. His body was still healthy, but it had changed in an unprecedented manner- one which it was correctly suspected might be something to do with Amy's supernumerary nipples.
As the months wore on, Timmy would find his pubescent development was continuing to change him in very different ways to most boys. At first it was fairly innocuous- he felt attraction to other boys instead of girls, and figured he must be gay, which he didn't feel was a big deal considering he basically couldn't have children anyway. But soon he realised his fantasies about men didn't feel gay- he felt like he wanted them to get him pregnant, to have a body that could bear and nurse children. It felt like his body was telling him he was not a boy but a girl, and the idea seemed really appealing to him.
Gradually his body transformed into her body. Rather than growing much taller and more muscular like a boy, he gained a little height and muscle and started to form a curvaceous figure. Instead of his shoulders widening, his hips widened. He developed mammaries, his nipples growing and turning sensitive while soft flesh grew on his chest. And unlike normal boys, his penis never grew but shrank. Eventually it had receded to a small nub, and he didn't even pee from it, the hole having moved lower down. To his surprise, as it shrank it became more sensitive- when he'd first discovered masturbating he'd jacked it between his fingers, but eventually he just had to rub it with one finger, or run the shower head against it. His scrotum had changed too, as it sank into his crotch and eventually formed a slit along its centre which became a vagina.
As he changed, Timmy felt less and less like a boy, and the changes felt less and less uncomfortable and more and more right- arousing, even. Sometimes he fantasized about his changes happening rapidly, like a werewolf transformation, or being dirty-talked to about losing his manhood. Something he noticed in particular was how he started to feel instincts about how to be a girl, fantasies that comforted and aroused him, ideas about what felt good to do with his body.
Slowly in his head those instincts convinced him to adopt a new identity- after all, soon he wouldn't be Timmy or even a 'he' anymore, so it was important to find a 'she' to be. She decided on the name Tammy, it was close to her old name and she liked how it sounded.
About 18 months after that fateful day he menstruated, Tammy asked to tell everyone at a school assembly about her being a girl now. Obviously she left out all the gross details and just explained she had slowly realised she was a girl and not a boy, and asked everyone to respect that. But the relief she felt when everyone applauded her, and she sat down next to one of her friends who told her "well done", was the most wonderful feeling of her life.