Doctor Fate buries the eldritch energies of the Commander beneath the Pentagon. Unbeknownst to all parties, they are under observation, by the Monitor. The Monitor explains the situation to his assistant, Lyla. Theoretical physicist, Joshua Champion, had opened a portal into an alternate dimension. Champion was immediately possessed by the Commander. In an act of resistance, Champion imparted a portion of the Commander's power upon his family. The Champion family contacted the Justice League of America for help. Working with the Justice Society of America, the Justice League of America set out to oppose the Commander.
Unbeknownst to their teammates, while on the Commander's home world, the Flash, the Starman, and Superman fell under the Commander's sway. The Commander becomes aware of the Monitor's observation. The Monitor turns his attention away. Upon returning to Earth-2, the Flash, the Starman, and Superman attack the Justice League of America, the Justice Society of America, and Supergirl. The Commander reveals that he is still in control of Joshua Champion. Fighting against the Commander's control, while fighting their teammates, is slowly killing the Flash, the Starman, and Superman. Joshua Champion's daughter, Victoria, nearly drives the Commander out of her father.
The Commander attempts to subjugate Victoria, but her Aunt, Meredith, bolsters Victoria's psychic resolve with her own. They reach for Champion's son, Ian, to add his strength to theirs, but Ian turns away. The Justice League of America, the Justice Society of America, and Supergirl, restrain the Flash, the Starman, and Superman. With Doctor Mid-Nite's blackout bomb masking her actions, Wonder Woman binds the Flash, the Starman, and Superman in her Lasso of Truth. Wonder Woman orders the three heroes to focus only on resisting the Commander. Finally accepting that the Commander is not actually his father, Ian adds his psychic fortitude to Meredith, and Victoria.
The Justice League of America, the Justice Society of America, and Supergirl, offer their own psychic strength against the Commander, Still, it is not enough. Only when the Flash, the Starman, and Superman join in the resistance, is the Commander finally driven out of Joshua Champion. Doctor Fate cautions that the crisis may not be over. As if on cue, the Commander emerges from the cloud of eldritch energy beneath the Pentagon. The Commander reveals how formidable a foe he is. The Justice League of America, the Justice Society of America, and Supergirl, battle against the Commander. Doctor Fate, and the Champion family, open a portal to the Commander's home dimension.
The Justice League of America, the Justice Society of America, and Supergirl, try to force the Commander through the rift. The Monitor turns his eye, once more, upon the Commander. The momentary distraction allows the Justice League of America, the Jusitce Society of America, and Supergirl to succeed in pushing the Commander through the rift. Rather than face eternity trapped in a dead zone, the Commander commits suicide. The power released by the Commander's death, propels the Justice League of America, the Justice Society of America, the Champion family, and Supergirl through time and space.
Ultimately, they come to rest in the inter-dimensional space that houses the Crime Syndicate of America's prison. Knowing where they are, Superman gets everyone back to their proper dimensions. The crisis passed, the Champion family decides to take a vacation, exploring the many alternate dimensions they just witnessed.