In Last Rites we see what happens in Gotham City during the time between Batman's abduction at the Hall of Justice (in Final Crisis #2) and the complete onslaught of the Anti-Life Equation which occurs sometime within a month after the close of Final Crisis #3.

Batman is missing - the remaining members of the Justice League have placed an all points bulletin for his whereabouts. Nightwing is finding that Batman has left some pretty big shoes to fill. Having recently captured Two-Face and placed him back in jail, he is aghast to find out that Harvey Dent has already re-escaped. To make matters worse, a Two-Face imposter has begun a crime spree across Gotham which brings Dick on a mission that will take him to the furthest corners of Gotham to a section of the city still left in shambles from the Gotham Earthquake.

Meanwhile, Tommy Elliot has re-emerged following the events of Heart of Hush. While on the mend he uses his recent facial re-construction surgery to his benefit and begins impersonating Bruce Wayne, siphoning funds from Wayne Tech corporations across the globe. During this time he runs afoul of Catwoman who with the help of Nightwing and Robin has Tommy re-captured and brought back to Gotham. Because Tommy now looks exactly like Bruce, Tim and Dick decide that they cannot simply place him in Arkham for fear of undoing everything Bruce had worked for. They decide instead to take him to a hidden section of Wayne Tower. There Tommy Elliot is held in a secret prison known to only Alfred and the boys where he is monitored by camera 24/7.

Finally Nightwing is left considering whether or not he should continue as Nightwing or don the mantle of the Bat. Meanwhile, Tim is still tying up loose ends from the gang war that has erupted in Batman's absence and finds himself dealing with Jason Todd and his one-time mentor Lady Shiva.