(Spoliers ahead, avoid if you have yet to finish Xenonauts)
The High Praetor is the title held by the commander of the Alien invasion, a Praetor.
The High Praetor is in charge of the invasion fleet, and observing humanity's efforts to combat the invasion force. It is the High Praetors decision to see if humanity should either be exterminated or subjugated, and is using the invasion as a pretext to test humanity. The High Praetor resides on board the dreadnought in his throne room, he exhibits a unique blue glow and a orange cape that denotes his status as the High Praetor.
The Xenonauts deduce that if the High Praetor dies, the invasion fleet would be thrown into disarray and would fall apart. By itself however all that would accomplish is the arrival of a second invasion fleet. However coupled with the Hyperspace Inhibitor, which would block all Hyperspace travel near Earth, this would destroy the invasion fleet and secure Earth's safety against the Alien Empire.
If the Xenonauts are able to activate the Hyperspace Inhibitor, the High Praetors dreadnought would descend down to Earth to unleash thousands of Reapers on Earth, as part of a contingency plan, that would however leave the High Praetor vulnerable to a Xenonauts insertion team aimed at assassinating the High Praetor, his death would spell the end of the invasion.
It should be noted however that it is impossible to capture the High Praetor alive. Any attempts to do so will result in the High Praetor playing the same animation as when he is killed and disappearing (effectively killing him).