Spider-Man: Edge of Time is a follow-up to Shattered Dimensions, and similarly it has more than one Spider-Man takes a starring role. Here, it is the regular, classic "Amazing" Spider-Man, and Spider-Man 2099 – in a story awash in time travel, temporal battles, and Anti-Venom.

The backbone of this story seems to play out more like a Spider-Man 2099 story, since he is the only character truly aware of the happenings in the game, and the changes that both Spider-Men encounter. From the opening, things are bleak for Amazing Spider-Man who begins the game nearly dead, and 2099 is the only one who can help. A new villain Walker Sloan enters the picture with a plan to rebuild the past (from the year 2099) in his image and design, which turns to affect both Spider-Men. From this point, chaos unfolds in typical comic-book fashion with gameplay evenly split between Amazing Spider-Man and Spider-Man 2099, with every other level interwoven with the events of one Spidey to the other.

The gameplay itself is a fairly typical arcade-style, comic book beat-em-up formula generally in line with modern beat-em-up games. There are large numbers of new moves to learn and purchase in the Upgrades menu, and several unique attacks and combos as each Spider-Man plays somewhat differently, and requires different strategies for their combat and use. For instance, Amazing Spider-Man plays a bit stronger and has wider-ranged distance attacks, whereas 2099 is all about speed. By collecting Golden Spiders, players can upgrade the health and defense attributes of the Spider-Men, and by collecting Portal Energy strewn about the levels, and from combat, players can upgrade the combat abilities of both characters.

Both characters have a stamina bar which allows each to use a quick-evade move, or a variety of much more powerful combat techniques. Beyond this, there is an icon besides the life and stamina bars fills as players run through enemies during combat which allows them to use a power known as the Time Paradox, which freezes time and enemies in an area immediately surrounding either Spider-Man.

Besides the regular story, there are a wide variety of bonus features. The secondary gameplay feature is called the Web of Challenges which drops players into specific points of the game to accomplish various tasks such as collecting all the Portal Energy in an area in a set time limit, defeating a number of enemies in a set time limit, building combos, and fighting without getting too beat up. Web of Challenges events are spotlighted during regular gameplay, and players are given the option to see the details of the challenge in-game, or to just continue playing. Either way, their results are still recorded during the initial playthrough. Other galleries and features include an action figure (character model) gallery, with history notes on the characters, a concept art gallery, a movie gallery (for the FMV's in the game), collected newspapers (with timeline altered headlines), and memos from Walker Sloan.