In the game's original ending, Electro shouts "Top of the world!" after he departs his battle with Spider-Man and he goes to the North Tower of the World Trade Center, thus giving Spider-Man the clue he needs to track him down for the game's final battle. When the towers were destroyed on September 11, 2001, the game was quickly pulled and re-released with a new ending, in which Spider-Man just happens to correctly guess the unnamed building that Electro goes to for the game's final boss battle. Furthermore, to make the resemblance to the World Trade Center less obvious, a bridge was added to join the towers together and the textures were altered. The original version of this game is now a sought after collectors item, but identifying it is exceptionally difficult.
At the end of the video game, The Mighty Thor is credited with defeating Electro in the final battle. This is because Thor was supposed to appear in an video segment in the video game where he talks with Spider-Man shortly after he has defeated Hyper-Electro, thus giving Thor the credit with Electro's defeat in the Daily Bugle newspaper. This was removed because the game's original ending takes place atop the World Trade Center towers when the game was being developed and it was removed because of the towers' destruction on 9/11. However, it appears that this segment was actually very close to being finished before it was removed.
After defeating Shocker, there is a cut scene where Spider-Man says that he doesn't need pointy ears and a cape to do his job. This is an obvious reference to DC's Batman.
One major difference in this game compared to its predecessor, Spider-Man (2000), is the presence of ground levels. This game presented levels that are city streets confined within a grid.
In this game, the black web lines on Spider-Man's costume are rendered much better than they were in the previous game, Spider-Man (2000), and he even has webbed armpits on his costume.