The player commands a team of up to six elite soldiers on the Axis or Allied side, undertaking a variety of missions. Once the player begins a campaign, they may select a premade character or create their own to lead the team through the game. Once the introductory mission is complete, the player can access a base complete with a medical station, armoury, personnel, and a panzerklein hangar. From this point, the player may select a team of six characters from a pool of 20. Each character has a role such as medic, sniper, scout, grenadier, soldier or engineer. Each role has different advantages and liabilities in battle. As the player progresses through the game, the armoury will receive new weapons for the player to use, either stolen from enemies or contributed from their own forces.
Silent Storm depicts a wide variety of the authentic weaponry and equipment of circa 1943 with great detail. Mixed into otherwise realistic elements is a plot that features secret weapon projects reminiscent of spy-fi, including energy weapons. Most notable are the Panzerkleins (pseudo-German for "little tanks"), crude powered armour suits.
The game features a remarkably advanced physics model. Nearly all structures are completely destructible. This has many tactical effects in the combat. For instance, if a character hears an enemy moving in an adjacent room, they can simply fire through the wall to attack them. Silent Storm also employs ragdoll physics for bodies according to the precise velocity of an impact. Fully three-dimensional mapping allows for obstruction calculations and cover effects from all angles, bullets ricochet and their stopping power depends on the weapon. The effects are exaggerated for a more cinematic experience (a hail of non-fatal bullets only make the target shake, but a single fatal bullet can send the target flying).