The story includes several major plot developments regarding Superman: the death of Superman's adopted father Jonathan Kent, the return of the pre-Crisis bottled city of Kandor, and the return of the original Silver Age incarnation of the supervillain Brainiac.

In the present, the Daily Planet is having a staff meeting attended by Perry White, Lois Lane, Clark Kent, Jimmy Olsen, and Ron Troupe.

Brainiac's ship arrives over Metropolis and sends out probes which everyone, including Supergirl, does their best to fend off.

Supergirl is also caught at this point and brought to Brainiac's ship just as Metropolis is encased in a bottle and a solar-aggressor missile is fired towards the Sun.

Although no one is hurt by the explosion itself, Jonathan Kent suffers a heart attack and dies in Martha's arms, just as Clark arrives.

Clark looks over and sees Bruce Wayne and Alfred Pennyworth standing under a tree nearby, and after a moment with Lois, he then retreat to his family barns, where he is devastated by the loss of his adoptive father.

The original cover depicted Clark and his adoptive father outside the Kent farmhouse apparently holding what may be beer.

The next week, DC reprinted the issue featuring a cover in which the label on the bottle was changed to read, "soda pop".

[4] DC Universe Infinite has cited the "Brainiac" story arc on Twitter as one of the comic book stories that served James Gunn as an inspiration for his upcoming DC Universe (DCU) film Superman (2025).

[5] Injustice 2 loosely adapts the comic in the opening scene of Brainiac taking Kandor.