Halo Novel...onyx?

I have read the first three halo novels..fall of reach is events before halo 1...the flood is bically halo 1...first strike is between halo 1 and 2....where does this new onyx book come in?....i know its about the spartan III project...but what really confuses me is that it mentions spartan IIs...didnt all spartan II get killed except for Master chief spartan 117 John?....and the other spartan ..i forget her name but she was near death and the Doctor lady ran away with her and the key artifact thingie.....Im sorry Ive read the first three novels a long while ago.....names pop in here and there but I got really confused reading reviews about this new onx book....can annyone catch me up?....summarize?...did I miss annything in th eother novels that will explain why there are more spatan IIs alive?