Taken to the police station for not carrying documents... please, help!

[minader]

Hi everyone. This story might be a bit long, but if any of you has any knowledge about Japanese law, please read my post and if you can, give me advice. I would be very grateful!
This is what happened:

A few days ago I was stopped by police while I was riding a bike in Tokyo. I was with my brother (just arrived to Japan) and we were stopped because the light on his bike was not working.
I am a student at a Japanese university, while my brother came here to visit Japan for holiday.
After asking us a few questions about the bikes, they also asked us to show them our documents (in my case the resident card while the passport for my brother).
Unfortunately I only had my 学生証 (Student ID card, a card with my name, a picture of me and the period of study written on it) while my brother had absolutely nothing.
When they found out we had nothing else, the two policemen called other policemen, which arrived almost right away by cars. After asking us a few questions, they said they could not let us come back home and that they had to take us to the police station!
It seemed my student card alone was not enough, and despite the fact we are living near from the place they stopped us (about 4 KM) we were not even allowed to go take our documents and bring them there (I tried asking but it seems it was not possible).
At the police station they made some copies of my student card and asked me some other questions in a room, alone. Another policeman told me clearly that what we had done is very bad and that we had broken a Japanese law.
Honestly I was speechless. I couldn't believe that only having forgotten a document would be such a serious matter (and it's not that I had absolutely nothing, the card I had with me did prove that I am a student at a specific Japanese university).
Anyway, after this, they told us that they would have come with us to my dormitory room to see if we actually had our documents (my brother is staying at my room and so his passport was here).
When we arrived here, the policeman took pictures of the dormitory, of the door of my room and even of me while opening the door.
Next we found our documents and we handed them to him, who then called the police station to inform the others.
Unfortunately that wasn't the end. The policeman said that I had to come back to the station again while my brother was allowed to stay at my room.
Now the best part: at the station they told me I had to write down on a paper what had happened during the day (to know what to write in details, they let me talk with an English native speaker on the phone, since I'm not fluent in Japanese), I had to sign several documents and lastly they even took picture of me from every angle, like the ones police takes of criminals. Now this was getting humiliating other than ridiculous.
After spending two hours at the station, they told me that I had to come over again the next Sunday in order to be questioned again with the help of an interpreter (I'm not even an English native speaker so an interpreter will be available only on the weekend).

This is the story until now. Today I read a similar story on the internet and the events were exactly the same. At the end, the guy who forgot the documents had to appear in front of a court but was dismissed without any penalties since he bowed low and was very sorry for what happened (he appeared at the court even with an apologizing letter). However, they told him that for what he did they could have put him in jail or that he could even be kicked out of the country (for anyone interested, here is the full story: Gaijin Card - DON"T Leave Home Without IT!)

Now I am getting more and more scared about this. And appearing in front of the court is not the only thing I'm worried about.
Firstly, when I had to write on that paper what happened during the day, they asked me to write also that I was aware of the fact that not carrying my resident card was illegal. However, since I thought that this might worsen my condition, I refused to write it and I told them that I thought that my student card alone was enough (which I have to admit is actually the truth, since that card has my name, a photo and the name of the unversity I am enrolled in - if I have that card how am I supposed not to have a resident card? It doesn't make any sense).
However now I am afraid I made a mistake. Maybe it was better to say that I knew it was illegal and that I just forgot the resident card on the dormitory. I'm planning to tell them this on sunday...
Secondly, another problem: the bikes we have are not registered with our names (in Japan it seems that having a bike is like having a car). One of the bikes was given to me by a friend who left Japan two weeks ago (I have no documents of it) while I bought the other one from another person on June, when he left Japan (this person was not Japanese, and he bought the bike used from a Japanese guy - I have documents of this bike, but it is registered to this aforementioned Japanese guy which I don't know).
Being things as they are, I am afraid that that the fact that the bikes are not registered to us might worsen my current condition. Furthermore, at the beginning the first two policemen that stopped us found out that the bikes were not registered with our names, but then the topic seemed to have been simply dropped when they asked for our documents.
Lastly, the biggest problem: this friend of mine who is staying in my room is not actually supposed to be here. In my dormitory even visitors are not allowed.
However, many people here invited friends/relatives from their homecountry and did exactly the same thing, without having any problem whatsoever. No one ever found out.
Despite this I'm very scared about this because, as I read from the story I talked about before, the questioning I'm going to have on Sunday will be very detailed: it will take from 2 to 6 hours and maybe a second one will follow; I will be asked any kind of questions, including questions about my relatives, their names, ages etc., basically everyting. If that's the case they are likely to find out about him living here even though it is not allowed.
Now I don't know that to do... do you think he should leave? In that case, he should leave now or it would be better to wait? Maybe I can say that he came here not permanently, but just for a few days, while looking for a better place to stay.
But I'm also thinking that maybe police doesn't care about this dormitory thing, since it regards only the university. Do you think it would be possible?
Another unclear matter is why I was the only one asked to go again to the police station and to be questioned on Sunday... haven't we done exactly the same thing, breaking the law?

I'm very scared about all of this. I'm afraid I might be kicked out of the country with no chances of ever coming back. I have still 6 months to spend here and I was already planning on coming back in the future.
I know that my problem is very specific and probably you can do little for me, but please if you have any advices I would really love to read them.
I just don't know what to do.

[RadioKid]

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.

[RadioKid]

DO you mean bicycle by "bike" ? not a motorcycle?

You need neither license nor insurance to ride on Bicycle.

I think you are suspected to be a bicycle thief.