Thirty-five years into the future, Brother Eye has managed to transform the majority of superheroes into cyborg bugs. As the last remaining heroes launch one final attack on Brother Eye’s power source, Bruce Wayne creates a time machine in an attempt to prevent Brother Eye’s ascension and this future. Before Bruce is able to use the time machine, he gets ambushed by cyborg bugs, forcing Batman (Terry McGinnis) to travel through time instead. Arriving in the past, Terry realizes that he has arrived five years too late, with what he was trying to prevent already in play.
Terry is then attacked by the cyborg bug of Plastique, which he subsequently dismantles. Deciding to break into the Terrifitech Tower to keep Brother Eye deactivated, Mr. Terrific’s building design begins to lock in, forcing Terry out. Retreating and disguising himself as a homeless man, Terry places the cyborg in a shopping cart and begins to slum outside of the Terrifitech Tower. Mr. Terrific then begins to grow paranoid, and after unveiling his newest invention, the uSphere, starts to ponder how to take care of the new Batman figure. As the Key, Coil and Plastique plan to break into Terrifitech to steal the uSphere, Terry overhears their conversation but is confronted by Terrific.
Transforming into Batman, he briefly battles Terrific but is forced to retreat and abandon the cyborg. Terrific collects the cyborg and realizes that while it is Earthborn, is far too advanced to have been built in present day. Terry then decide to join up and manipulate Key, Coil and Plastique, making a heist team with the three. After playing on the feelings of the public, Terrific claims the new Batman Beyond to have been a multiversal alien, and despite hating himself for using integration for his own goals, Terrific reveals he plans to stop this Batman Beyond. After Key watches Terrific’s broadcast, he and the rest of the heist team turn on Terry.
While traveling in The Bleed, The Carrier is destroyed and the Stormwatch team is killed. On Earth, SHADE gets wind of this event and sends Amethyst, Frankenstein and Ray Palmer to investigate. Sending them through the Phantom Zone, they are attacked by Black Adam who cuts off Frankenstein’s arm. Arriving at the Carrier, Palmer replaces Frankenstein’s arm with that of Hawkman, who is then revived by the Nth Metal. After finding a distress signal from another surviving member of Stormwatch, Hawkman, Amethyst and Frankenstein go to an unknown planet to investigate. There they are attacked by robots, who are revealed to be led by a Brainiac-controlled Engineer.
Grifter is tracking down killing an alien race known as the Daemonites who are hiding on Earth disguised as humans. Due to him being the only one able to see aliens, King Faraday captures Grifter after his power evolves and allows him to see and determine which Universe somebody is from, if they have powers and whether or not they are lying. Sent to Cadmus Island to work with Fifty Sue and Deathstroke, Grifter winds up attacked by a stealth OMAC and teams up with Sue to find it. Grifter’s partner, Justin, then retreats to Voodoo and learns Faraday is after her as well.
Responding to a distress call from Green Arrow, Jason Rusch is desperately searching for his friend Ronnie Raymond, finding him with his girlfriend. Jason then drags Ronnie into the Firestorm Matrix and flies to Seattle. To their horror, they find that Green Arrow’s lab has been completely destroyed as he lies dead amidst the rubble. After Arrow’s funeral, Ronnie refuses to let Jason out of the Firestorm Matrix for weeks. Upon finally doing so, they end the Firestorm arrangement and Jason gets working on a transporter while Ronnie begins drinking. Even a JLA attempt to get the two working together again fails.
In Futures End, the New 52 Captain Atom appeared twice and the Bronze Age Captain Atom (with Blue Beetle and Dr. Spectro) appeared once. It may have been the end of the New 52 Captain Atom. Time will tell.