Red Energon is an extremely powerful substance of Energon. It can give a Cybertronian the power of hyperspeed and the ability to slowly freeze time for a few moments, although it takes significantly longer to refine than regular Energon. If any of the humans made contact with Red Energon, it could harm them greatly.
After obtaining the red energon, Starscream used what was left of it in the Harbinger to refine it. Though he managed to get about half of it, he remarked it was only enough for 1 dose, or maybe 2. He used it to retrieve another relic that could be of use to him.
Starscream also used the remaining substance to go through the groundbridge and steal the three Omega Keys from the Autobots' base. The Red Energon eventually wore off and left Starscream to fend for himself.