Basically Shisui got set up by Danzo/Anbu. Danzo brought him their to fight, while Shisui thought it was just a meeting. Danzo attacked Shisui and the reluctant Shisui not wanting to fight , still put Danzo to sleep with a 3 tomoe genjutsu. Danzo broke the rules of a Leaf Shinobi fight; they were supposed to agree on it like Naruto and Sasuke did at the hospital. Shisui won round 1 and Danzo won round 2 along with help, although the fight was supposed to be over & should have never happened. Its like Itachi letting Sasuke win their bout. One wasnt trying to hurt the other , while the other was out for a "kill" or in this case "eyes". Or its also like when Konan planned a trap for Tobi before he was even there.