Starglass by Phoebe North
My darling daughter,
Know that I never would have left the Earth if it hadn’t already been doomed. . .
The generation ship Asherah coasts through space, bound for a planet its passengers have never even seen. On the eve of their arrival, sixteen-year-old botanist Terra discovers that her orderly society has fractured. Walking home one night through the long-abandoned engine rooms, she witnesses the murder of an innocent man. Now, called on by the Children of Abel, a group of rebels intent on destroying the High Council, Terra must prove her mettle–assassinate the ship’s rising captain. In order to carry out her task, Terra must betray her father, deceive her teacher, and challenge everything the Council has ever taught her was true.
The rebels think that Terra has nothing left to lose. But when she falls for Silvan Rafferty, the boy that she’s meant to kill, Terra learns that “doing your duty” isn’t always as easy as it seems.