Centipede: Infestation is, like Space Invaders Extreme or Pac-Man: Championship Edition DX, a modern "re-imagining" of a classic video game franchise. Here, players are thrust into a post-apocalyptic wasteland adventure where plant and animal life has largely been eradicated by war, and bugs have been mutated to monstrous sizes.

Rather than directly playing like classic Centipede games, Infestation plays somewhat more like a modern dual analog action title like Geometry Wars or the way classic Robotron was intended to be played. Players move with the Nunchuck Control Stick or 3DS Circle Pad and aim and shoot with either the Wii Remote or 3DS touch-screen (the Classic Controllers on the Wii allow for straight dual-analog control). Gameplay takes place within a single staged area that is often not much larger than the area allowed by a television screen and merely face off against swarms of incoming bugs, and eventually, the pivotal centipedes themselves. The centipedes generally appear as boss encounters for single stages, and their behavior--moving back and forth, having body segments that can be targeted individually--is a direct homage to the original games.

Unlike the original games from the early 1980's, Infestation delivers a wide variety of weapons available to the players. Flame Throwers, Freeze Throwers, Laser Guns, Machine Guns, Lightning Guns, and others are on hand for players to maximize their bug-blasting potential. Each player may carry up to four different weapons at one time, and each weapon can be upgraded one time by collecting it a second time. Weapons are assigned to the A,B,X,Y buttons or D-Pad (Wii Remote), and once activated, can only be used for a limited time, which forces some strategic hoarding and saving of weapons for bigger encounters. However, weapons cannot be carried over to the next stage and players will start with their standard Pea Shooter.

Several different types of bugs will appear during stages, each with different strengths, attacks, hit points, and behaviors. Ants, for instance, do not tend to attack directly, and will generally follow set paths. Aphids will drop swarms of babies if not killed fast enough. Bomb Spiders explode... like bombs. Grubs appear in large numbers to be nuisance, and so forth. There are also wasps, caterpillars, scorpions and others, including boss monsters. New weapons are dropped by small spiders dropping in from above. Other bugs will drop seeds which grow into defensive plants such as a Gun Turret or a Bomb Plant which launch attacks against bugs, adding to the overall firepower and offensive capabilities of the players. These weapons remain where they fall and attack enemies automatically.

The story largely revolves around a group of survivors on post-apocalyptic Earth, one of whom named Maisy may hold the secret to returning plant life to the planet. The story progresses over 40 stages, which deliver a variety of different challenges beyond simply killing everything onscreen. Sometimes switches must be hit, sometimes specific enemies or weapons are highlighted. Each also features character development and plot points divulged during cutscenes between stages, most of which are simply dialog between the main protagonist, Max, and Maisy. Max's brother Rivet appears early on, largely to fill the role of a second player during co-op play. Numerous characters and costumes are unlockable over the course of the story. Besides characters and costumes, other unlockables include art galleries, movies and music. There is also an in-game achievement list known as Accomplishments, and after every stage is completed, players will be informed of which Accomplishment has been unlocked (if any) with a number identifier.