The story opens with Tom Traven, a haggard-looking rebel guarding a mostly abandoned resistance outpost. The rebels he’s with are suspicious of him, as he asks them again for a man named Roy Keller. They brush him off, saying they’re only bringing him along as they have orders to gather every rebel in the area – but they don’t know him and they certainly don’t know this Roy person. Tom settles for the night, opening up an old diary covered in the scrawled down notes of a madman “What did she see?”. The main handwriting a neat, delicate hand by contrast – it’s the diary of his wife, Anna Traven.
We flashback briefly to the night of her death at the hands of Combine soldiers, the Overwatch, in a derelict old apartment building, breaking down the door before we cut away.
As Tom goes on reading the diary, Anna’s voice over tells us how an advanced alien race known as the Combine have conquered the Earth, in an event known as the Seven Hour War. Through flashbacks we see how only six months after the war, he and Anna were forcibly relocated to City 17 by the new regime. Anna explains that the war was the byproduct of a failed teleportation experiment in a research facility known as Black Mesa, which opened a gateway to another dimension and led to the Combine finding Earth. No one’s seen what they call “the Combine” themselves per se, only their war machines and the UN-led peacekeeping Conscripts. The US has been decimated, global governments dissolved, most of everyone relocated to anonymous numbered cities for safety, away from the dangerous alien wildlife now infesting the countryside. The Black Mesa administrator, Dr. Wallace Breen, has become the puppet dictator as all blame for the Black Mesa Incident was shifted to a Dr. Gordon Freeman, who has since disappeared.
Once in City 17, they meet Roy, Tom’s childhood friend, and Norman, Roy’s older half-brother and they both get involved with the remaining insurgents and first resistance movement. During dinner, Roy proclaims to be pro-Breen, extoling the virtues of the Conscript-led state and sanctuary cities keeping them safe. Drinking heavily, Tom becomes belligerent, insisting that no one elected Breen to his position and they don’t know the true intents of the Combine. Anna agrees with Roy initially, arguing that the Combine must’ve kept them all alive for a reason.
Anna, an idealist, soon allies herself with David, a celebrity pacifist who sees the situation, while less than ideal, as an opportunity to unify mankind for a common cause of rebuilding society while the Combine’s true motives are as of yet unknown. He seeks to establish civil rights and a unified civil form of governance, cooperating with the rule of the Combine and Dr. Breen for their protection.
Tom, a reactionary, instead allies himself with Roy and Stanley, a Marine Corps colonel who was there in Black Mesa and is hellbent on undermining the Combine occupation and on delegitimizing Dr. Breen’s rule through armed insurgency. During their first town hall meeting in a church, Tom gets close to Stanley by thwarting an attempt on his life by Barney Calhoun, a former security guard of Black Mesa. Barney reveals that the military didn’t try to save the facility, they tried to kill everyone involved to keep it from going public. Whoever they didn’t kill, they left for dead for the nuclear bomb that followed. Stanley denies having anything to do with the nuke, saying that was “the suits’ call”. Barney is beaten to within an inch of his life and left, as Conscripts converge on the church and set it ablaze.
Back in the present day, Tom is introduced to the main surviving branch of the resistance in the rebel base New Little Odessa. He reveals his intent to find Roy and kill him, as Roy was the one who betrayed his wife, Anna Traven, and turned her in. Everyone reacts with varying degrees of incredulousness – Anna has since become a mythic figure, “the founder of the resistance”, but no one knows much about her or if she even existed. He proves it by handing over his wedding ring, their names inscribed on it.
He says he needs to retrace his steps to find Roy, as years of Combine deliberately drugging the water supply has rendered his memory hazy and unreliable, along with everyone else. He’s unclear how much time has even passed. A medic, Zoe, talks to him about the diary, how he knows Roy killed her. Tom notes that the last paragraphs, addressed to Roy, state as much. She called him out, alone and in the dark with his mistakes. He doesn’t understand much of the last passages, but that part he can understand. Zoe asks if he’s read it already none the wiser, what does he hope to gain from it? He answers that every time he reads it, he remembers a bit more, seeing it play out in his dreams.
Then the Combine suddenly attack the base, Tom helps fight them off. It’s revealed that the rebels are planning an attack against the Air Exchange, a facility dedicated to replacing Earth’s atmosphere with a toxic one as a final blow to human rule over the planet. Tom reveals that he was part of the construction of the Air Exchange years ago, and convinces the rebel leadership to let him take a guide position of the expedition, going on foot to a smuggler’s boat up north ready to take them up the river.