A civilization created the child AI (citadel) the Reaper and the Mass Relay's.
Now, why the child. It's probably the Citadel reading Shepard's emotions/mind/whatever and taking a form that he will understand. Shepard was beaten up and he lost all hope. He was thinking how he couldn't save anyone. He though about the child.
So the Citadel AI took the from of the child.
Why didn't it help the Reaper in the first part? The Child AI probably doesn't much control over the Citadel. If it had, it would have simply killed Shepard before he even close to the control panel. It was probably added by the creator to explain to the race why the cycle has to end.
Joker/EDI and Quarian/Geth are just few example in a long lasting war with each other. The Geth are synthetics. They will think logically. If they ever need to have war with the organics, they will. But the organics are illogical. They will wage wars for unimportant things. Hell, wars were waged because just 1 woman. They are currently in an alliance (and only if you played your cards right) because both races are in danger. The Geth know that the Reaper will try to make them their slaves and destroy them at the end of the cycle. They have every reason to fight the Reaper. It's just that they have a commune enemy that they are in peace. Do you really think that the peace would last long?
I do think that the Geth wouldn't start a war, but I do think that the other, organic, races would either try to take over their territory, them or just start a war. The Geth will defend them self.
Also, about the Arrival.
In that DLC, you destroy a Relay with physical damage. That disables the magnets on the 'mass field' (dunno what the blue mass is called) which expands with extreme speed and caused insane damage. The blue mass is something like plasma. Those magnet keep it in one place and concentrate the energy in the mass relay.
But at the end of the game, the Citadel sends one orange beam to the Mass Relay. I think that the beam does 2 things.
First it sends a command to send the same beam to the next relay. This causes the chain reaction.
The other action is that it changes the blue field into an orange. This also probably changes it's characteristics.
Now when the self destruction command starts, the blue field is released. Unlike the blue one, this one doesn't deal huge physical damage, but more of an EMP style damage.
That's why the solar systems aren't destroyed.
Just my opinion about the whole stuff.
EDIT: Also, there is a HUGE difference between the Geth killing organics and the Reaper doing the same.
The Reaper will NEVER extinct all organics life. The will harvest advanced organic life when other, less organic life have a change of evolving further.
On the other hand, we don't know what the Geth or other synthetics could do in a war. They could kill ALL organic life forms. Not just advanced but all. The Creator though that organics and synthetics can't co-exist. So they separated them. The allow organics to live until the point where they could do something seriously retarded and then "restart" the universe.
EDIT2:
Stop calling it space magic. Even the best scientists of the universe don't fully understand how the Mass Relays work. They don't know anything about the Keeper, the Citadel and about many other things. The reaper tech. is thousand times more advanced than the best tech the other races have. BioWare didn't explain how it all works but they don't really have to. Did they explain how the Citadel work? No? But why isn't anyone crying about that?
Yes, it would be nice to know exactly how it worked, but it's also nice to have some holes to fill with your imagination. Filling all holes in a huge story like Mass Effect would require another 10 parts of the game just to explain shit, without any story. Just explaining stuff.
Sorry, but you guys ask to much. Don't be a ***** and turn on your brain cells. I remember the old time where I even had to imagine the whole story for a game and I still have fun. You guys have everything, don't like it a bit and now you QQ.
Lets call the wambulance. (ノಠ益ಠ

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