This reads like you've not paid any attention to the game, or not actually played it.

The Rachni Queen is completely explained, if you save the queen in ME1 it's the same queen that has been forced by the reapers to breed corrupted children again. If you don't save the queen in ME1 the queen in ME3 is a reaper abomination of genetic manipulation, much like the Protheans vs Collectors. There is a difference in what happens if you save the queen in ME3, if you didn't save the queen in ME1 you get a reduction in readiness points because the reaper made queen goes off the rails.