90's movie about one boy and two friends

It’s an adventure movie, from the 90’s or maybe early 2000’s, and I don’t remember much of it. I watched it on TV a loooong time ago. There was a boy who had a rich father, and I guess this father was an inventor. This boy meets two other kids, brother and sister, who apparently are orphans and whose adoptive parents have trained them to become kind of ninjas/spies/something like that. There is a scene in which they jump from a tree on top of the car their friend (the protagonist) is in, and enter the car through the window. There is some kind of mystery they have to solve, and I think one thing one of the kids (I think it’s the girl) needs to do to follow the villains is enter the trunk of a car, but the kid gets nauseated and has to “train” not to get sick inside of a trunk. At the end of the movie we find out that the villain works with the father of the boy, and I THINK there’s something related to an invention or a bomb made by the father.
I remember really liking the concept of those two orphans raised by adoptive parents who trained them to become ninjas, but I don’t remember much of the rest. Please help me! :slight_smile:

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