In Commandos 2 the player takes on the role of an allied officer in charge of directing a group of commandos, each with a different set of skills and abilities that they can use, who take part in a series of twenty-one missions – two training stages to get used to controlling the commandos; ten story missions; and nine bonus missions that feature unique challenges and situations to complete, but are only accessible after each story mission is completed, if the player acquires a set of books marked "bonus" within each of them. Each mission in the game features a series of objectives, divided between main and secondary, that the player needs to complete in order to finish a mission, including securing an escape route from an area, as well as clues to where players can find supplies or locate useful assets to help them with their mission; while briefings for each mission outline most objectives and clues, others are provided through completing current objectives or clues the player has knowledge of (i.e. if an objective is to contact someone and the player completes this, the contact might provide an additional objective and/or clue for the player to use).
Each mission features the player having control of a subset of commandos, though in some missions, the player begins with a few commandos to use, but can gain control of others through either contacting them somewhere in the mission's location, or rescuing them from imprisonment. The original six from the previous game are once more available for use, though some have a few notable improvements in how they can be used – the Green Beret can now climb telephone poles and traverse their cables, can jump out of windows, and can carry small containers around; the Sniper can climb up telephone poles to use them as sniping positions; the Spy can now not only direct soldiers and lieutenants to look somewhere else, but can order soldiers and enemy staff to move somewhere else if disguised as an officer, while his syringe can now daze, knock out, or kill an enemy, depending on the number of doses they are given; the Diver now kills enemies by throwing knives at them, and now carries a grappling hook that can be used to traverse walls or set up a tripwire to knock out enemies; the Driver can now set up traps, both lethal and non-lethal; and the Sapper can now use a mine detector to find buried land mines and disarm them, as well as set-up mines to eliminate infantry and armoured vehicles. Along with these six, the players also gets control two new members to use, including: the Thief, who is the most agile of the group, can climb in and out of windows and through small holes, hide in tight spaces, climb and traverse telephone poles and cables like the Green Beret, and unlock metal containers and some doors with his lockpicks; and Whiskey, a dog who the commandos can use to trade items between them, as well as bark near enemies to distract them. In addition to the commandos, players also gain control of allied units, most of whom can be equipped with weapons and placed in four different combat stances, including firing out of windows and crouching down, and thus be used to combat enemies when needed.