FALLOUT 3 QUEST SPOILERS BELOW
There has been no truly official word either in game or otherwise, on what they are looking for. Some people speculate it's more FEV, but then that raises the question of why are the particularly in Downtown D.C. when it could be anywhere, and why they would look for more, since they seem to have enough in Vault 87. Other's say they may be looking for more people to mutate into super mutants. This one especially makes no sense. If they have been in downtown D.C. for years, and they are seeing essentially no people to mutate exceot Brotherhood, who usually kill them or are killed by them, instead of captured. Even if they did capture them, I don't think the mutants are smart enought to remove the power armor other than pulling them through it which would likely kill them.
Now, there is a third group who say that the mutants are searching for something we are not aware of at all. A special weapon, virus, etc...etc... This one seems most likely since we don't know what this unknown factor is so we have no arguement for it, whereas the other two idea's have some pretty concrete arguements that they are not true.
Maybe Bethesda will do a 6th DLC about it, since in the interview they said they believe Mothership Zeta to be the last one, but they thought the same thing with Broken Steel. Maybe it will be better explained in Fallout: New Vegas (Unlikely, since their on the other side of the....."country"...) Or, more likely it would be explained in Fallout 4, if it takes place on the east coast. However, they way I see it is if they don't anounce new DLC for it, then I don't see it being revealed any time soon, if at all.