All across the world, atomic energy ceases to exist. Wally West joins his mentor, police forensics scientist, Barry Allen, in Central City. Incredibly, Allen has invented a time machine. Using his "cosmic treadmill", Allen, as the Flash traveled into the future. In the year 2287, the Flash finds humanity on the verge of being wiped out by alien invaders. Moving faster than the eye can see, the Flash learns that the aliens, known as the Dokris, have sent a radiation absorbing "hive" back into Earth's distant past. With the hive rendering all atomic elements inert, mankind can never develop atomic energy, or atomic weapons.
Without their atomic weapons, the humans of the future have no way of defending themselves from the Dokris. The Flash sends West, as Kid Flash, back to the year 100,842,246 B.C. Kid Flash's mission is to find the Dokris hive, and destroy it. Meanwhile, the Flash returns to the year 2287 to aid humanity against the Dokris. Upon arriving in the past, Kid Flash encounters a giant, web-spinning ant, which has entangled a human-headed bird. Kid Flash frees the strange bird-creature, then tangles the ant up in it's own web. Kid Flash begins his hunt for the hive. Suddenly, Kid Flash is attacked by a giant bee, which stings him, and carries him into the sky.
Spying a nest of the bird-creatures, Kid Flash begins vibrating at super-human speed, to drive the bee lower. As Kid Flash had hoped, the bird-creatures come to his rescue. Despite the language barrier, Kid Flash is able to convey to the bird-creatures how important it is to him to find the hive. Flying off in multiple directions, the bird-creatures join the search. Kid Flash is just about to join the hunt, when the delayed effects of the bee's stinger paralyzes him. In the year 2287, the Dokris have ferreted out the location of a large concentration of humans. The Flash tracks the humans to an abandoned series of caves, once known as "Colossal Caverns".
The Flash convinces the men hiding there that soon their weapons will be functional again. The Flash lures the Dokris hunters into an old monorail tunnel, then seals them inside. One Dokris hunter comes up from the rear and floors the Flash with a radiation blast. After telepathically probing the Flash's mind, the Dokris leader, Mynher, offers the Flash the opportunity to join the invaders. When the Flash refuses, he is imprisoned in a cell, one which continues to bombard him with the enervating radiation. The Flash keeps pulling the trigger on an atomic pistol, anticipating the moment when Kid Flash completes his assignment.
At last, the atomic pistol discharges, blowing a large hole in the cell wall. It takes every last shred of strength the Flash has left to stagger out of the cell. Once free of the radiation field, the Flash's super-speed returns. A power he puts to good use, battling against the Dokris. Joined by the human resistance fighters, now armed with fully functional atomic pistols, the Flash is able to drive the Dokris off Earth. Returning to the present, the Flash learns the details of Kid Flash's mission. Having discovered the hive, the bird-creatures provided an antidote to the bee's paralytic stinger. Once back on his feet, Kid Flash destroyed the Dokris hive, restoring atomic energy across history. The crisis past, the Flash and Kid Flash, as Allen and West, meet up with reporter Iris West, for dinner.