40 years before the Humans' arrival, the Reapers existed already. The reapers had issues with constant attacks from other species: leading to the decimation of their attack forces and population.
20 years ago, after a attack that nearly destroyed their city. The Reapers decided that it would be beneficial to move the academy as a precaution, should they be attacked again, in hopes of protecting the future generations.
15 years later, the Humans arrived. The Reapers had a city by this time and, now reinforced and prospering, ally with the new species.
Recently, the Reapers are working as the law keepers of the city's working in a similar manner to police.