Like the earlier Superman - Spider-Man crossover, the issue is noncanonical, as it assumes that the heroes and their respective cities of residence, Metropolis and New York, exist in the same universe.

There is one brief reference to the earlier crossover story, when Peter Parker sees Lois Lane in Metropolis and recalls meeting her previously in New York.

Superman vs. the Amazing Spider-Man was very much a collaboration between the two companies; this second treasury-sized edition was largely the work of Marvel, with DC's approval.

The first team-up featured the heroes' most popular enemies, Lex Luthor and Doctor Octopus, but with this story writer Jim Shooter clearly sought plot convenience over "rogues gallery" prominence, and chose Doctor Doom (more typically a Fantastic Four villain, though he had occasionally battled Spider-Man and would do so in the future as well) from Marvel, and the Parasite (a lesser-known Superman foe) from DC.

The book was officially co-written by Shooter and Marv Wolfman, who at the time was writing the popular DC title The New Teen Titans.

Easily dispatching the criminals, his Spider-sense alerts him about a nearby construction site, but unable to determine any immediate danger, he moves on.

The reader learns, however, that the site camouflages an elaborate base of the Latverian monarch Doctor Doom, connected with a years-long plot of his known as "Project Omega".

Peter Parker goes to work for The Daily Planet while Superman's alter-ego of Clark Kent takes a leave and joins the staff of the Bugle in New York City, each seeking to investigate the crisis from a different end.

Doom captures Wonder Woman before they can accomplish anything, however, while Spider-Man escapes and trails her captors to their destination, finally learning the truth about Project Omega.