Flux is a fictional character in the Skannerz universe. According to the instruction manual for the original Skannerz Flux was the first person to discover the aliens on Earth and the inventor of the Skannerz as a way of tracking and capturing the monsters for the purpose of keeping them from blowing up the Earth like they did to their own planet. Throughout the manual Flux gives advice to the player through "Secret Flux Hints"
Flux comes back in the Skannerz Commander instruction manual when the aliens apparently have given up the three original tribes and are now trying to form their own tribes, so Flux invented the Skannerz Commander to trying and control the rogue aliens.
For more information see Storyline.