It is a vision of the Reapers destroying everything organic in the Protean planets, but take a look at this video:
At 0:06, you can see something like a mouth opening and an animal scream. That can be a Protean being ripped apart and screaming in agony, but it seems more like an Organic creature attacking. I really think that there are entire races working for the goals of the Reapers, some of them hoping to be spared against the whole galactic xenocide of the Reapers or some other undisclosed goal.
Of course there are other races that have been indoctrinated by the Reapers. If you talk to Vigil on Ilos, he explains the pattern of the Reapers, and how they usually destroy organic life from start to end:
Use the Keepers to activate the Citadel Mass Relay to usher in the Reaper fleets
Reapers destroy all opposition in the Serpent Nebula, and gain access to census data, intelligence, files, and other critical info concerning sentient races.
Cut off communication/relays among all systems, leaving them alone and fragmented
Systematically exterminate planets, one by one
Indoctrinate primary and secondary species that are anti-Reaper, and release them as refugees to remaining colonies
Harvest resources for hundreds of years
Return to dark space, leaving a single vanguard to prepare for the Reapers' return in 50,000 years
So it's likely that the Prothean vision contained other indoctrinated species. Although we always hear about the Protheans, and their demise, it's likely there were other, lesser-known sentient species that lived alongside the Protheans, that were in the video, attacking the Protheans.
It'll be interesting to see if there really is just ONE Vanguard in the galaxy.
Though you'd thing if the Reapers left a second it would have assisted Sovereign.
Actually there really needs to be another Vanguard, or maybe another way for the Reapers to interact with the galaxy to continue to pave their return. With the keepers control overriden and the threat of the Citadel Relay neutralized, they would also have to find another way inside the galaxy, as i said in a previous post, another gigantic Mass Relay can be lying in wait in an unexplored part of the galaxy. Also, since we don't trully know the origins of the Mass Relays (Reaper origin or the first civilization origin), maybe the council races will find indications on how to build one of their own and launch a pre-emptive strike against the dormant Reapers.
