A Prothean Beacon is a piece of ancient Prothean Technology. They were a form of communication that could sent messages directly from one Prothean's brain to another. In modern times, finding a Prothean Beacon that's still intact is extremely rare. So when a team Systems Alliance scientists discovered one on Eden Prime they sent out the SSV Normandy captained by David Anderson to recover and protect the Beacon. Their are two known beacons in Mass Effect, one on Eden Prime and one on Virmire.
 Eden Prime
By the time Normandy landed on Eden Prime, Saren and the Geth had already attacked the planet and moved the Beacon. Once Saren had used the Beacon he left and set charges all over the station. Commander Shepard and his team arrive at the station and manage to deactivate the charges before they blow. While waiting for the Normandy to pick you and the Beacon up, one of your squad mates (depending on your gender) will move too close to the Beacon and get sucked into it's power. Shepard will throw them out of the way and take the full effects of the Prothean Beacon himself.
The Beacon shows Commander Shepard flashing images of the Reaper invasion that exterminated the Prothean race. The Beacons weren't designed to sent messages to a human mind so it wasn't clear to Shepard what the vision meant. It also overloaded his mind and knocked him unconscious.