Codename: Gordon presents an alternative to the storyline of Half-Life 2, with locations inspired by both Half-Life and Half-Life 2. Along the way, Gordon Freeman — the protagonist from the canon games — meets with some of the main characters of the Half-Life series and tries to find what caused the disappearance of the third dimension.
The game starts with Gordon Freeman in a dock area. After making his way through a few zombies and headcrabs, Gordon meets with Barney Calhoun, a prominent character in the later Half-Life titles. He tells Gordon of an "entire dimension" missing and also notes that the science team is working on solving the problem. Being injured, Barney cannot leave the place, so he gives Gordon his pistol, telling him to leave without him.
In the second chapter, the player meets with Eli Vance and his daughter Alyx who tell Gordon to take their car, which will help him reach City 17, as seemingly it is the center of the problem. They also tell him to talk to Dr. Kleiner, about his new invention, the gravity gun. Soon after, the player finds Dr. Kleiner, who tells Gordon about his worries regarding the missing dimension and also gives him the gravity gun mentioned by Eli and Alyx.
After being attacked by an alien gunship and getting past a prison heavily guarded by Combine soldiers, Gordon manages to reach City 17, where he finds the G-Man. He tells the player he has been expecting him and claims to not be behind the situation regarding the missing dimension, instead he says he is but a "lowly pawn in a shady game being played by sinister powers". Soon after, Gordon confronts a strider — a large tripod assault unit — which turns out to be the source of the problem, as upon defeating it a portal is opened; stepping into this portal, Gordon is sent back to the third dimension.