Over 50,000 years ago, Javik was one of the last remaining warriors to survive the Reapers' destruction of the Prothean empire. On the planet known in the next cycle as Eden Prime, Javik and hundreds of thousands of other Protheans were to be put into cryostasis, so that they would outlast the onslaught of the Reapers, and could later reclaim the galaxy. Unfortunately, indoctrinated soldiers stormed the cryostasis facilities, and only his cryo-pod survived.
In 2186, Commander Shepard and his crew uncovered Javik's pod among Prothean ruins while investigating Cerberus activity on Eden Prime. Shocked that he was the last Prothean alive, he decided to join Shepard's quest against the Reapers.