Protocol to be used to make microcontroller to work as mouse
As mentioned in comments the HID (Human Interface Device) class is what you're looking for to operate as a mouse without any special drivers. You can find the full specifications at  HID Related Specifications at USB.org although they're fairly heavy reading.

Your best bet to get started is probably to buy a development board that contains a USB compatible microcontroller and has a vendor supported USB stack available. Both the AVR and PIC series have one available if you're after a small 8-bit solution, but many vendors provide the same.

As an example recently I purchased a Microchip Low Pin Count USB Dev kit that came with complete working examples that made getting started easy. While I was using the CDC class I noticed it also included an example for a HID mouse.