what do you mean have it output with COM ports? What is a COM port? I'm familiar with a usb port, but what is a serial port?
Look at and read the SoR tutorials. The subject is covered.
Also look in the Windows Device Manger and there is a Ports(COM & LPT) category. Then Google will tell you tons about each.
As to your original question:
If the PC, with Jave, is doing the 'high level' behave for the Bot, this would send commands from the PC (serial transfer) to the Bot. The Bot would need an 'embedded processor' to receive and interpret the 'high level' commands then set output bits to control motors, LEDs, etc to enable the Bot to execute the commands (express emotion, speak, etc).