As far as M1 goes galactic civilization reaches a certain evolutionary point then the keepers on the citadel activate the citadel (remember it's a huge mass effect relay) bringing the reapers into the galaxy from outside the galaxy. The reapers do their thing then retreat back through the citadel into dark space. The protheans were able to figure out a way to hide on Ilos until the reapers had left the galaxy, at which point they used the conduit to gain access to the citadel's control area and modify the keepers so that they wouldn't summon the reapers. As it turned out it was actually a reaper who told the keepers when to summon the rest of the reapers so when the keepers ignored him(Sovereign) he had to figure out a new way to activate the citadel relay, which was to send an agent(Saren) through the conduit, to undo what the protheans had done.