In around the 6th book the amerlin ( who deposed swan, but whose name I can't think of right now) was basically enslaved by one of the chosen. Now I am reading crown of swords and the Amerlin is no longer subject to the Chosen. I can't remember what happened to the chosen that was calling shots. Please remind me what happened.

Don't believe Siuan was ever captured by a chosen.

@galadin,

 

elaida a'roihan deposed siuan sanche and became amyrlin,she was,albeit indirectly,

under mesaana control,this situation was true until the gathering storm chapter 41.

later,(towers of midnight),egwene and mesaana fought in tel'aran'rhiod and mesaana

literally lost her mind,post last battle,she is drooling somewhere in the white tower.

She wasn't enslaved, just being manipulated.  Alviarin ws taking orders from Mesaama on what to make Elaida do but she left for a little bit (don't remember why).  In that time ELaida was able take control again and have Alviarin removed as Keeper.  Mesaana was still in the tower when Elaida broke free of the manipulation.  Elaida by that time wasn't really important to her plans anymore.  The chaos had been sowed, the ajahs mistrusted each other, Asan'gar was to help ensure there would be no peace, Elaida screw ups with the BT and trying to capture Rand would be know to the tower sooner or later.  Alviarin even mentioned once Elaida's blunders were known to the hall she would probably be removed.  Mesaana job by then was to mostly ensure the tower wouldn't unite with the rebels.