We actually don't know much about Rachel Duncan yet, except the fact that she's a "proclone," and has been raised all of her life completely aware that she was created in a laboratory. She seems to have some sort of job at the Dyad Institute (remember, this is the laboratory where the clone experiment began), but it's not clear exactly what she does. Whatever it is, though, her gig requires her to wear high stilettos—seriously, those things are killer.
When we meet Rachel at the end of the season, she offers Sarah, Cosima, and Alison "contracts" that will supposedly ensure they'll never be contacted by the Dyad Institute, and that they'll be protected from the Proletheans and Helena, who want them dead.
While Alison accepts the offer, fearing for her family, Sarah does not, despite the fact that Rachel subtly threatens Kira, saying she will be in danger if Sarah does not work with the Dyad Institute.
When Sarah returns to Mrs. S's home to see Kira, she finds both Kira and Mrs. S gone. Like a plotline out of a Liam Neeson movie, they've been taken. It's assumed Rachel had something to do with the kidnappings.