Following the period of instability caused by the events described in Half-Life, an interdimensional organization known as the Combine invades the Earth, defeating the human forces in the Seven Hour War. A Combine Citadel is erected in City 17, a town in Eastern Europe reminiscent of World War II ghettos. Dr. Wallace Breen, a human scientist, rules the city on behalf of his new masters. An energy field prevents humans from procreating, and no new children are born. Earth is turning into a grim, oppressive police state.

Meanwhile, Gordon Freeman, the man who was at the center of the events that took place shortly before the rise of the Combine, awakens from his stasis and is inserted into a train to City 17 by the mysterious G-man. Gordon is soon brought into a resistance group and makes a seemingly futile attempt to bring down the Combine and liberate the Earth.

Half-Life 2 is a linear first-person shooter with light puzzle-solving elements and many setpieces, similar to its predecessor in concept. The player guides Gordon Freeman through City 17 and the wilderness that surrounds it. On his way, he'll encounter a few friendly characters, but also fight dangerous foes. The game features a realistic physics system: Gordon can pick up objects and toss them freely, and many of the puzzles are physics-based - for example, at one point the player has to weigh down a seesaw with bricks at one end to turn it into a ramp.

Gordon's enemies, apart from alien wildlife which found their way to Earth, are mainly Combine forces, which utilize a variety of firearms, gadgets, and vehicles. Policemen and foot soldiers work along with helicopters, gunships, and gigantic walking machines to hunt him down. To defend himself, Gordon has a range of weapons available: from the iconic crowbar for close-quarter fighting, through pistols and rifles, up to grenades and a rocket launcher. One of the most notable weapons is the gravity gun, with which Gordon can pick up objects, hold them in the gun's anti-gravity field, then hurl them at the enemy with great force.

Setpieces in the game include coordinated assaults on enemy bases, fighting gigantic boss enemies, bringing down aircraft with the rocket launcher, and others. A few levels require the player to navigate buggy-type vehicles. Some of the more exotic stages involve the player summoning an army of antlions to unleash on unsuspecting foes.

Included with the game is Counter-Strike: Source, a version of Counter-Strike made with the new Source engine which powers Half-Life 2, and Half-Life 2: Deathmatch, an online multiplayer game featuring the same physics and weapons as the single player game.