So how do brakes work, exactly?
Here's a quick sketch of the brake caliper: it's a fancy chamber. And a fancy C-clamp. That's all a basic brake caliper is. The chamber accepts the piston, and there's a direct connection between the incoming fluid line, the chamber and the piston. As the pads wear down, the piston moves out, and you need more fluid in there to keep it all working (and keep air out), which is why brake master cylinders have reservoirs.
The C-clamp part is basically what the fluid pressure works against. The piston moving out under hydraulic pressure presses on a pad (or pads), which press on the brake disk, which presses on the inside pads, which press on the fixed side of the caliper. The whole caliper slides on a couple of pins so that it can center itself over the brake disk.
In addition to all that (not that this applies to the EX250), some bikes have fancy brake calipers. This can mean more pistons, or pistons on both sides, or multiple brake pads on a side, etc. They're all variations on the same "C-clamp and fluid chamber" idea. On the EX250, only one side moves. One brake pad is pushed by the pistons, the other brake pad just kind of sits there on the other side of the rotor.
The brake fluid comes directly from your pedal or lever, into the fluid chamber on the caliper, and pushes directly on the piston. The fluid seal keeps the fluid from leaking out. It's a simple, but reliable, design.
If the piston is pitted or scratched, it can rip up the fluid seal, which leaves you with brake fluid all over your bike.
A brake caliper really is about four parts: caliper body, two seals, and the piston. (Well, two seals per piston, and however many pistons per caliper.) That's it.
Not surprisingly, disc brakes on a car work the same as on your bike. For more information, see howstuffworks.