So in issue #3 Kid Flash was resurrected when we find out the Legion was able to snatch up his essence at the moment of his Death as the Flash. In issue 4 we learn that when Bart helped push Superboy Prime into the Speed force back in Infinite Crisis it accelerated his aging process, hence he became the New Flash for a while. Braniac 5 reveals that had the rogues not killed him he wouldve died in a matter of years due to his accelerated aging. The Legion used the Lightening Rod device to capture his Soul, and restore him to his proper age.
At the beginning of the issue, you see Starman (in modern times) digging up a grave and you just see the word "Kent" on the gravestone. Apparently Starman dug up the body in the grave and placed it in the same healing chamber that healed Superman when he "died" at the hands of Doomsday.
Apparently, it took a thousand years, plus the strand of Luthor's hair that Polar Boy took from the past in Smallville to do it but...
...Conner Kent is back from the dead and starts brawling with Prime declaring it "round three". The last page of the issue reveals that Superboy-Prime and Time Trapper are one in the same. Time Trapper is the older version of Prime and he's been the one trying to destroy the Legion and remove them from Superman's life. He reveals that he remembers his battle with Conner and that he knows he already won
Superboy lives again!