Project shadow started out as Armageddon's Spec ops division. It was lead by agent stavropol. Much of it is shrouded in mystery. After the collapse of armageddon Shadow became an independent project and started recruited.
Later on shadow hijacked and took many ships, creating a fleet. The PS Ravage heads the fleet. Also geth dreadnoughts and flood dispersal ships have joined. As well as the reapers.
In the beginning the crucible was to be constructed to destroy the reapers. Well stavropol has instead used it to take control.