Button presses on the Game Boy case translates to touches to the phone’s screen beneath them. The buttons have a conductive sheet at their base so that the phone’s touchscreen senses button presses as it would finger taps.
As for the open window that corresponds to the Game Boy’s screen, the patent states that the games being played will be scaled down to fit that window, almost as if you’re actually playing the classic Nintendo handheld. There’s also a smaller window up top for the front’-facing cameras and speakerphones.
If Nintendo intends to actually make something out of this patent, then it’s likely some day we’ll start seeing Game Boy emulation in some form on smartphones. But that is a major if, because being granted a patent doesn’t actually guarantee that something will come of it. (Source: USPTO via Silicon Era)