Unlock towers: Each game the player is offered different choices of towers to unlock so every game will have different combinations and play styles.

Combine towers: Any two of the basic tower types can be combined to form a new tower with new mechanics. There are 55 different towers in the game.

Design the path: Walls can be placed to create a maze for the enemies to travel through. The player must arrange walls to give the enemies a long path while leaving good spots to place towers.

Adapt to the map: Maps are generated with blocked tiles which cannot be crossed by enemies or have towers built on them. There are 12 different ways the map can be randomized and the player must adapt to each new map.

For anyone who played Prototype TD 1, many mechanics have been reworked for the better. Enemies now have much more variety and are more interesting (8 enemy types, new randomization, better scaling). Blocked tiles can be cleared for a price, allowing much more interesting adaptation to the maps. Maps are more interesting and come in much greater variety. The worst tower types have been removed or reworked (Bridge removed, Shock, Coil, Tag reworked) and 2 new tower types added, Lightning and Sniper. Damage, range and speed boosts for towers now apply to specific tiles which makes them interesting and not overpowered. From 3 combination towers in the first game now there are 36 with many creative new mechanics and they are used together in each game. The overall balance of the game is much better, it is not possible to survive long beyond the final round no matter how good your luck is.