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作为对联合军掌权的回应，一群组织松散的游击战士、间谍和亡命者组成了反抗军，志在推翻联合军的暴政。抵抗军的力量不足以正面对抗联合军，因此他们致力于通过渗透国民护卫队、走私武器、输送难民等方式逐步削弱其控制。抵抗军建立了一条横跨17号城的“地下铁路（Underground Railroad）“网络，以帮助逃离城市的居民前往莱温霍姆、黑山基地东区、白森林以及海岸地区的抵抗军基地。另一方面，联合军也抓住一切机会毫不留情地镇压抵抗组织。联合军对莱温霍姆镇发动了大规模的猎头蟹炮弹轰炸，只留下了一名已知的幸存者。据 茱蒂丝·莫斯曼所言，尽管抵抗组织取得了一定程度的胜利，但联合军依然对他们的活动知根知底；抵抗军能够存活至今，完全是因为联合军不把他们当作值得一提的威胁。
戈登·弗里曼回归的五年之前，在城堡建设期间，联合军成功在17号城市隔离区的一栋公寓楼内定位了G-Man。联合军将G-Man匆忙囚禁在一个悬浮于隔离区上空的保险库中，由被捕获的 弗地冈人提供能量。联合军曾计划将G-Man转移至别的地方，但最终并未实现。伊莱·凡斯在发现了保险库的存在后，错误地认为里面关押的是戈登·弗里曼，并派出了女儿 爱莉克斯·凡斯去解救他。爱莉克丝突破了联合军的重重阻挠，最终击落了保险库并成功进入其中，误将G-Man释放。G-Man向爱莉克丝展示了她的父亲伊莱未来被联合军探员杀死在白森林的命运。作为释放他的回报，G-Man赋予了爱莉克丝介入时空进程的力量，让她杀死探员，拯救了父亲伊莱，并改变了《半衰期2：第二章》的结局。G-Man还告诉爱莉克丝她已经证明了自己的价值，足以替代另一名抗拒G-Man意志的“雇员”（暗指戈登·弗里曼）。最后，他将爱莉克丝置于休眠状态的无尽黑暗中，独自离开。
戈登·弗里曼穿过了布满蚁狮巢穴的海岸沙地，来到了 弗地冈人营地。在 弗地冈人盟友的帮助下，弗里曼获取了”虫饵“，一种能够召唤蚁狮群的信息素囊。弗里曼带领着蚁狮大军突破了诺瓦矿场的沿海防线，成功渗透进了监狱内部。蚁狮群在监狱里大开杀戒，将狱卒部队打得溃不成军，弗里曼借机到达了诺瓦矿场深处的联合军运输站，成功与爱莉克丝碰头。二人一起找到了凡斯博士与莫斯曼的位置，得知了后者的双面间谍身份。在爱莉克丝的胁迫下，莫斯曼不得不开启了运输站中的量子纠缠传送门，但在关键时刻她又背叛了二人，带着伊莱一起传送到了联合军的总部城堡。不得已之下，弗里曼和爱莉克丝在装甲核心士兵攻入的紧急关头试图传送到克莱纳博士的实验室。传送门在二人消失的瞬间爆炸了，并连带着摧毁了整个诺瓦矿场。这场大捷的余波传到了17号城市，进一步激发了市民的斗志。
迄今为止，抵抗组织都一直在联合军对城市外围和海岸周边的围剿中勉强苟活。然而当诺瓦矿场与联合军唯一的传送门被戈登·弗里曼一并摧毁后，抵抗军转守为攻，向联合军的总部城堡直接发起了进攻。Freeman and Vance's actions demonstrated to the civilians throughout City 17 that open aggression against the Combine would not necessarily result in the Resistance's annihilation, and that a full-scale uprising against the Combine could conceivably defeat it and wrest Earth from its control. Nova Prospekt was one of the Combine's most heavily guarded and impregnable strongholds, and Gordon Freeman and Alyx Vance, just two members of the resistance, assaulted and defeated the Combine on its own ground. While most Resistance troops attempted to liberate the city, Barney Calhoun led a mission to rescue Eli Vance, whom they learned from the Vortigaunts, was held captive in the Citadel. For over a week the increasingly large and determined resistance army was locked in bitter urban combat with the Combine forces, engaging in bloody street-fighting. Civil Protection found themselves hard pressed and unable to control the uprising, and Overwatch reinforcements were sent in. At the time of Freeman and Alyx's return, the Resistance was in control of suburban areas, while the Combine controlled the city center and other pivotal buildings. The city itself was heavily damaged from the toll of the battle. Despite the Combine's obvious technological superiority, it could not gain the upper hand over the Resistance cells.
Freeman and Alyx were lost in a teleportation loop for over one week, and all but presumed dead in the destruction of Nova Prospekt, but the civilian population of the City joined the Resistance en masse and began the uprising in their absence regardless. When Freeman and Alyx returned to the city, Freeman and Calhoun combined their leadership skills and began to turn the tide against the Combine. Freeman led the attack on some of the final Civil Protection barricades and CP-controlled buildings before using the city's tunnels to travel quickly to the city center. At this point, the Resistance were caught in an intense Overwatch counterattack. Resistance positions were bombarded by Headcrab Shells, destroyed by Striders, and tougher troops. The assaults towards the center of the city caused intense damage to the buildings, due to the Combine's usage of pulse artillery. Thanks to Freeman, the Resistance was able to overcome the attacks and press on to the city center after breaking through a generator-powered barricade. Unfortunately, Alyx Vance was captured by the Combine whilst scouting for a route on a rooftop.
Now in the city center, the Resistance launched an attack against the Overwatch Nexus, the center of Overwatch activities. Its capture was intended to impair Overwatch's movement and coordination, and open several gates for the resistance, as well as eliminate a powerful Combine Suppression Device on the roof. Freeman and Calhoun destroyed the power-generators and opened the building for Resistance reinforcements. The Combine attempted to recapture it with Striders, but following an intense battle, the Resistance, led by Freeman, defeated the Striders and secured the Overwatch Nexus. This allowed the Resistance to attack the base of the Citadel, where the Combine infantry was pulled back, and defense was turned over to the Striders and Gunships. The Synths inflicted heavy casualties on the resistance, but even they could not keep the rebels at bay; Freeman led the final charge toward a prominent horse statue, destroying two Striders in the process, and then penetrated the Citadel.
Once inside, Freeman allowed himself to be captured, arriving at Wallace Breen's office after having been stripped of his weapons. Mossman, feeling guilt at allowing Eli Vance to be captured, rebelled against Breen, apparently having only feigned her allegiance to him. She freed the captured freedom fighters, forcing Breen to attempt to use the Citadel's reactor to teleport to the Combine Overworld. Freeman overloaded the reactor, causing it to explode, killing Breen and tearing the entire top section of the Citadel away. Vortigaunts rescued Alyx and Freeman just in time, burying them in the rubble at the base of the tower. The damage inflicted on the reactor had caused most Combine technology in the city to come open to cybernetic attack, and the forcefields around the city dropped, allowing thousands of creatures to swarm in, mainly Antlions. A more widespread implication of the Citadel's destruction was a dampening of trans-dimensional Combine communication technology worldwide, isolating Combine forces on Earth.
The Combine began to withdraw their forces from City 17, leaving behind some infantry units and their reserves of Civil Protection forces to stall the Resistance's escape. Alyx and Freeman managed to partially stabilize the Citadel reactor, giving more time for the remaining Resistance forces led by Calhoun to evacuate. However, the Combine and the increasing swarms of Antlions were not making evacuation easy. The Combine reserves in the city were defeated in open battle by the Resistance or led away by Alyx and Freeman. They and Calhoun escorted the last of the citizens to the final trains of refugees evacuating the city. The Combine advisors were evacuated in escape pods just as the Citadel exploded, virtually annihilating the remains of the City and all those left within.
Battle of White Forest
The destruction of the Citadel had caused an infant Superportal to begin forming, which, once mature, would allow massive reinforcements from the Combine Overworld to pour through, alluded to by Eli Vance when he said, "It'll be the Seven Hour War all over again, except this time we won't last seven minutes!" referring to the fact that if these reinforcements made it through, they would easily crush the remaining Resistance forces, whom the Combine were now struggling to overcome. It was later revealed that this had been the Combine's plan since the detonation of the Dark Fusion reactor. However, Alyx and Freeman managed to obtain the data planned to be sent to the Combine Overworld, which the Resistance could use to close the portal. The Resistance forces evacuated their refugees and troops to the Resistance base of White Forest, where they were planning to use the Xen Relay Network to close the Superportal. Alyx and Freeman were forced to fight their way through the hordes of Antlions that had colonized the vast mines near White Forest. During their journey, they found they were advancing to White Forest in tandem with a large Combine force on its way to attack the base. Alyx was mortally wounded near a mine by a Hunter, but fortunately revived with the help of several Vortigaunts.
In order to beat the Combine to White Forest, Alyx and Freeman obtained a car to race there. At one point, they discovered an Advisor, but were unable to kill it before it escaped. Upon reaching the White Forest Inn, Combine soldiers supported by Hunters ambushed and attacked them but were fought off, taking heavy casualties. The two then reached White Forest, where they found a crashed Combine dropship carrying a single Strider, which was defeated by Dog. Alyx and Freeman turned over the data packet so Magnusson and Kleiner could make the final adjustments to their rocket. Soon after, Combine soldiers directed by an Advisor raided White Forest through the secondary silo, but again were repelled by Freeman and the silo was closed just in time. Soon after the raid, Magnusson realized that they could not finish their rocket before the Combine attacked. In retaliation to this adversity, the able-bodied Resistance members prepared for defense and Magnusson directed Freeman in the use of the Magnusson Device. This made real resistance against the Striders possible, since without the Devices the Resistance would have been forced to use woefully inefficient RPGs. The main body of the Combine attack, consisting of a company of Striders supported by packs of Hunters, launched their attack on the base. Making use of the Magnusson Devices, Freeman eliminated all the Striders, allowing the launch to go ahead safely. The rocket was launched and successfully used to seal the Superportal, stranding the remaining Combine forces on Earth.
Following this victory, Alyx and Freeman immediately prepared to leave White Forest to pursue Dr. Judith Mossman. The Resistance leaders discovered from the data packet retrieved by Alyx that Mossman had located the legendary research vessel Borealis. Mossman was in trouble and the two were determined to beat the Combine to the Borealis. Unfortunately, before departure, the White Forest Hangar was attacked by two Advisors, one of which killed Eli Vance before being driven off by Dog.
Due to Alyx's actions in opening the Vault and freeing the G-Man five years earlier, Eli's death in Episode Two is prevented. Consequently, at the time of his original death, Alyx is taken by the G-Man at this same moment and put into stasis to "await assignment". Eli and Gordon are left in the White Forest hangar, with the Advisor dead and Alyx missing. Eli expresses his frustration, vowing to kill the G-Man for this. He hands Gordon his crowbar, telling him "We have work to do".