i see it like this possibly
weir gets nabbed by the reps then brought into the fold
but shes still too human
so the underground takes her
but in the meantime her thoughts are being shared with the others and they realize the wraiths great weakness
while with the splitter group she becomes its leader
then she sets up the observation experiment as a total setup
shes the one who fierd the probe and shes commanding the ship thats destroying the fake city
all this to get the sga the tracking device so they can wipe out the reps once and for all allowing the splitter group to work unfettered as she said at the very end of the ep
"good now we can work without having to look over our shuolders all the time"
what do you think?