When I was a teen, one of my relatives when on a trip to Japan. As a sourvenir, he brough me a manga. Being in Japanese, and the internet not so popular, I never had the chance to ever know what I was reading.

According to my relative, he went into a shop and asked for a manga as a gift. According to the store clerk, that was "the most popular manga at the moment", but well, you know how these things work. All of this happened around late 90's and early 2000's.

I used to look at the drawings and making up my own plot. The only thing I seem to remember clearly is there at some point the protagonist was in a sort of museum, and monsters materialized out of nowhere. Then again, I have very poor memories about it.

This manga has been long lost but ever since it has bugged me what the hell was it. So to summarize, I´m looking for:

A (suposedly) popular shonen manga.
From between late 90s and early 2000s.
It features a fight with monsters in a museum.

I know these are very faint clues but I don´t know of a better place to ask

the only manga I remember that has something like that is Petshop of horrors but it's not shounen (nor does it look like it is). I also can't comment on its popularity

Could it be Gantz? There are a few scenes like that and the time period seems to fit.