ME1 - learning about the mystical beings called Reapers that are a major threat to the galaxy and actually defeating one.
ME2 - a bunch of nonsense with no connection to a previous game but in the end defeating a human baby Reaper.
ME3 - uniting the galaxy and fighting the Reapers.
So guess which one is the overarching plot here that is in common for all three games. You must be thinking it's breaking the Reaper cycle. Nope. The Catalyst tells us that the overarching plot of the series turns out to be synthetics rebelling against organics...Do you see now why 'the Catalyst' part of the game is so stupid and doesn't fit into the series?
Over simplification of things.
ME1- Learning about the game world including about the conflict between Quarian and Geth that nearly wiped the Quarians out of existence and left the galaxy preparing for possible war with them. Then under the leadership of Saren and Sovereign the latter of which is believed to be a pure synthetic AI lead the Geth in massacring any organic that gets in their way of their goal.
ME2- You learn not all Geth thought like the group that attacked organics how ever they did stood by and did nothing while they attacked organics. You also get a quick learning in how Reapers are created, why they need so many bodies harvested and what ultimately happened to the Protheans. As well as fight a giant Reaper fetus.
ME3- Reapers finally invade you try to unite the galaxy to fight them and build the Duce Ex Machina machine. During this the conflict between organic and synthetic still shows up as the Quarians rather then channel all their efforts into facing the Reapers choose to channel all their efforts into again picking a fight with the Geth. Which might have gone well if they picked literally any other time in history. Geth panic and ally with Reapers were they go to far more extreme lengths then Sovereign did to control them. Legion agrees to help you with every action it taking being for the benefit of the Geth first and Quarians second.
If Geth/Peace option is used then the Geth assist in building the Crucible and fighting the Reapers because the Reapers are still the over all threat uniting everyone against them. Had the Reapers not existed the Geth would have gone back to their normal set up of wanting to be left alone.
Destroy ending you never learn what would become of this new set up with the Geth due to them being wiped out. Meaning any and all socialization improvements over the years with them are removed any if a new race of synthetics is created they will be completely different.
Control ending leaves Shep AI with the ability to prevent the violence from escalating to species killing levels. Conflict might or might not happen but if it does Shep and about 4 dozen Reapers will show up and tell everyone to knock it off (Paragon) or simply blow up a few buildings to make it's point (Renegade)
Synthesis blends organic bodies and synthetic parts into a new form better. Starting a new level of evolution for organic life in the galaxy. And putting them on par with the eveolution of synthetic life so one can not fully surpass the other.