They did. That is what ME 1 was all about. The protheans modified the keepers which usually activate the citadel rely. The keepers didn't respond when it was time for the cycle to begin so Sovereign had to go there to activate it. That is why Saren and the Geth were enlisted. The geth were supposed to replace the keepers as a servant for the next cycle. We stopped them. They had to travel to the next closest rely through dark space. And that is when ME3 picks up.