Bryan had been sleeping when he woke up needing to use the bathroom but what happened is that while walking to the bathroom he was only partially awake and bumped into his little sister.
He helped he up and then went into to the bathroom and he had to sit because he had to let a log go. But what happens is that while on the toilet he started to shrink and regress.
It was after he slipped into the toilet that he became fully awake and was surprised when he was having trouble getting out of the toilet.
The men in black go in and dart Bryan who falls asleep. They then transfer him into a plastic bubble and then get ready to leave when Bryan's mom sees them and ask where they are taking her daughter. They tell her that Bryan had been infected with a virus that has left him where if he comes into contact with anyone or thing that he will take and copy them some way.
They then say that for the next month he will be infectious to himself. They say that the virus dies out 3 weeks with no new contact they then say that after the virus had run it's course that her son turned daughter will be able to be returned to her along with information how to get a check to care for Bryan.