Do you have the license to ride on bike? It is illegal to ride on bike without having license in Japan.
Also it is illegal for foreigner to walk around in Japan without resident card. You could be imposed fine at most 200,000 JPY. It is clearly stated
on this page at Q41 in Japanese (unfortunately, I could not find corresponding English page).
And the bikes. Can you prove those bikes are not stolen by you or by your brother? Police can investigate if the bikes are stolen or not after troublesome investigation. They will check the bikes and trace how the bikes are treated and check the story with what you will tell on Sunday.
Also the bikes without documents are very troublesome because they could not have the mandatory insurance. For some kind of bike, it is illegal to ride on it without insurance.
As for your brother, Police could find he is innocent because he arrived at Japan very recently and has no time to steal bikes.
You should have to be very careful when you get bike in Japan. Bike is dangerous vehicle not only for the rider but also for the other people around the bike.
I personally think your brother is safe in your dormitory if the manager of dormitory allows. Police will check your story about the bikes until they convince that you own the bikes legally.