Where to begin, I chose destroy as I had already aligned with the Quarians.
Indoctrination is not what happened, I am utterly convinced of that now. The planet Joker lands on is not Earth, the twin moons in the sky confirm this. Besides if we follow the chain of events they clearly show us multiple mass relays blowing up first. Now, there is a mass relay in the Sol system, and if the
Arrival is anything to go by, that means Sol, and every major fleet in the galaxy is now dust. Buzz Aldrin is Joker IMO, the twin moons confirm this for me.
Now StarChild, and the Reapers. I think that StarChild is a AI that was left behind by those that created the Reapers. From what he says I can only assume that his creators created synthetic life forms that rebelled, much like the Geth. I also think that they were on the loosing side of that war, because why else would they need something like the Reapers. So this ancient race created the first couple of Reapers to combat their synthetic problem. But in classic organic style they put StarChild in charge. StarChild pulled an EDI and became unshackled, the Reapers turned on the creators (

) and started harvesting them for the "good of their species". This crazy circular logic (the only way to save is to destroy ala iRobot) breaks something in StarChild and it becomes convinced that the only way to go about it is to harvest advanced civilization.