Wait, there's one more major revelation to remember from season one. Moments before Sarah heads down to meet Rachel and sign the "contract" that will supposedly protect her and Kira, she gets a call from Cosima:

 
 
 
 
 

So, that's why The Dyad Institute is shady: they own human beings. 

Sarah emails Rachel a short note: "Up yours, proclone," then rushes back to Mrs. S's home, only to discover that Kira and Mrs. S are missing. It's presumed that Rachel is behind this.

SEASON TWO, COME AT US, BRO.