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This article describes the Half-Life 2: Episode Two storyline, chapter by chapter. Continuing the plot of Half-Life 2 and Episode One, Episode Two consists of seven chapters telling the story of Gordon Freeman and Alyx Vance's journey through the Outlands to a large Resistance base named after the forest. After the destruction of the Citadel, the Combine are working to open a massive superportal to call for reinforcements. Combine Advisor pods have also been scattered throughout the region. The destruction of the Citadel, as explained by Dr. Kleiner's broadcast in Episode One, has caused a portal and communications blackout on Earth-stationed Combine forces, leaving them isolated and disorganized. A crucial part of the plot is the transmission packet which the Combine sacrificed the Citadel to send, a copy of which Alyx and Gordon stole before making their escape. It contains information relating to the location of the Combine Overworld and allows the creation of the superportal to be controlled from the "other side". This information has to be delivered to White Forest so that the Resistance can use it to shut down the superportal and prevent an even greater Combine invasion.
 Chapter 1: To the White Forest
Alyx Vance attacked by a Hunter.
The opening chapter picks up where Episode One left off. The Citadel Core gave out as Alyx and Gordon were leaving City 17, and the resulting shock wave has derailed the train in which they were traveling. Gordon and Alyx survive the crash, and Alyx retrieves the Gravity Gun in order to free Gordon from the wreck. The ruins of City 17 are visible, with a superportal forming above the collapsed Citadel. A portal storm occurs, appearing to emanate from the Citadel ruins, destroying the damaged rail bridge and opening a path into a mine shaft for Alyx and Gordon to follow.
Alyx informs Gordon that they must contact the White Forest base and deliver their data packet. They travel through a short Zombie and Antlion-infested mine tunnel to a communication building, and Alyx is able to contact White Forest base. Dr. Kleiner and Eli Vance are relieved to learn that Gordon and Alyx survived the detonation of the Citadel, and Dr. Magnusson is introduced as the head of the White Forest base, more concerned with the data packet than the safety of Gordon and Alyx. The sound of a hunter-chopper and an overheard Overwatch message confirm that the Combine are still searching for the duo and the data packet Alyx possesses.
Shortly afterward, Alyx is critically wounded by a Hunter. A Vortigaunt arrives in time to drive off Antlions and stabilize Alyx's condition. Gordon becomes separated from Alyx and the Vortigaunt and must travel through Antlion caves to meet them at a nearby Resistance outpost. It is during this cave journey that Antlion Grubs and Workers are first encountered.
 Chapter 2: This Vortal Coil
Reprogrammed Sentry Gun firing at Antlions.
Vortigaunts healing Alyx.
Gordon arrives at a small Resistance outpost within the mines manned by Griggs and Sheckley. The Vortigaunt has brought Alyx to the outpost and is awaiting the arrival of his kin in order to heal her wounds. Griggs and Sheckley introduce Gordon to the Antlion Detector, and, with the aid of reprogrammed Hoppers and Sentry Guns, are barely able to hold off several Antlion attacks until the Vortigaunts arrive. The Vortigaunts assist in dispatching the next wave of Antlions and proceed to tend to Alyx. The Vortigaunts are unable to save Alyx, however, without the use of an Antlion larval extract, so Gordon and his Vortigaunt companion travel deeper into the mine to retrieve it.
Gordon and the Vortigaunt discover a Zombie infestation, as well as an overrun Combine troop carrier accompanied by Zombines. As they travel deeper into the Antlion caves, they encounter the Antlion Guardian, protector of the larval extract. Gordon is forbidden from killing the Guardian for fear of spoiling the extract and hence must outrun the creature through the caves. He is able to avoid the Guardian and summon the Vortigaunt to the Nectarium where the extract is obtained.
They deliver the extract just in time, and the Vortigaunts heal Alyx. During the healing process, the G-Man contacts Gordon, stating that he has been prevented from doing so by the Vortigaunts until this point. He hints at Alyx's importance to his plans and reveals that he had saved her life at Black Mesa despite the objections of unnamed others (Dr. Breen's face flickers on the screen behind the G-Man at this point). The G-Man asks Gordon to escort her to White Forest safely and instructs an unconscious Alyx to tell her father to "prepare for unforeseen consequences."
After Alyx has recovered, she and Gordon, accompanied by the Vortigaunt, proceed to the surface.
The title of the chapter is a reference to the phrase "shuffle[d] off this mortal coil" from Shakespeare's Hamlet.
 Chapter 3: Freeman Pontifex
The last Victory Mine outpost.
Upon reaching the surface, a large group of Combine forces is seen traveling north towards White Forest with Advisors in tow. Gordon must fight off the Antlion Guardian, along with an Antlion Guard and several of their smaller kin, before reaching the last Resistance outpost of the Victory Mine. There, they find that the settlement has been overrun by Headcrabs. Gordon is required to descend into the zombie-infested mining settlement in order to reach a working car for the journey to White Forest. Alyx assists Gordon by covering his progress with a sniper rifle powered by the Vortigaunt. Gordon finally reaches the far side of the settlement where the muscle car awaits. He jumps the car over a broken bridge back onto the side Alyx and the Vortigaunt are waiting at. The Vortigaunt takes his leave of Alyx and Gordon, informing them that his kin are hunting "shu'ulathoi" still in their escape pods.
Pontifex is a Latin term meaning both "priest" and "Bridge Builder".
 Chapter 4: Riding Shotgun
Having acquired transportation, Gordon and Alyx proceed at top speed to White Forest. They discover a radio tower and Alyx decides to try and contact White Forest to warn of the impending attack. While establishing power to the transmitter, Hunters arrive and ambush them. Gordon fights the Hunters directly for the first time and manages to defeat them. Alyx and Gordon resume trying to contact White Forest base but are unable as Advisors appear to be blocking the transmission.
Continuing, a crashed Advisor pod is discovered by the road. Alyx and Gordon soon encounter the telepathic attacks of an Advisor. They investigate a nearby barn and discover an Advisor encamped inside it. Alyx exposes its life support system and Gordon damages it with the Gravity Gun. The Advisor emerges from its mechanical cocoon and demonstrates its telekinetic powers by pinning Gordon and Alyx to a wall. It appears unfamiliar with its environment, as it probes first a barrel and a dead rebel before nearly killing Gordon. However, further damage to its life support system forces it to flee. Alyx and Gordon fight off a Combine ambush and escape a Hunter-Chopper which arrives at the barn.
Gordon and Alyx are pursued by the chopper to the next Resistance outpost, the car's engine giving out as it breaks through a barricade at the entrance. Gordon defeats the chopper by firing its mines back at it, and the rebels at the outpost offer to repair the car.
 Chapter 5: Under the Radar
The White Forest Inn exterior.
While Alyx and the rebels work on the car, Gordon disables a Combine Autogun that is hampering Resistance movement. In the meantime, a rebel technician repairs the car and installs a radar detector that picks up Resistance caches. After the car is fixed, Alyx and Gordon continue to White Forest, traveling through the zombie-infested countryside and retrieving supplies from several hidden caches.
An enormous Combine ambush is laid for them at the White Forest Inn, but after defeating Hunters, soldiers, and Elites, they approach the White Forest base. They witness a dropship being downed by rebels, however the Strider that it was carrying awakens. Dog arrives and defeats the Strider, and Alyx challenges him to a race to the base.
 Chapter 6: Our Mutual Fiend
Isaac Kleiner, Eli Vance and Alyx Vance talking about the Borealis at White Forest.
The lodge being destroyed by a Strider.
Arriving at White Forest, Alyx and Gordon reunite with Dr. Kleiner and Eli Vance, and Alyx finally delivers the transmission packet acquired in Episode One to them. They also meet Dr. Magnusson in person, another former Black Mesa scientist who is egotistical, verbose, authoritarian, and holds a grudge against Gordon. Gordon and Alyx learn that the White Forest team is preparing a special rocket which they plan to use, in conjunction with Alyx's data packet and the satellite array launched during the events of Half-Life, to close the Combine superportal. They are interrupted when a Combine attack penetrates the base. Gordon defeats the attack force, consisting of Hunters and soldiers, and closes the silo doors that are allowing access to the facility.
After successfully repelling the attack, Gordon meets up with Alyx, and the two return to Dr. Kleiner and Eli who have completed decoding Dr. Mossman's message. It reveals that the "project" is none other than the Borealis, an Aperture Science vessel which mysteriously disappeared some time before and is rumored to carry powerful technology. Dr. Kleiner suggests using the technology of the Borealis against the Combine, while Eli insists that it be destroyed to avoid another Black Mesa Incident. Initially, Eli wants to follow Dr. Mossman to rescue her; however, he becomes convinced that his own knowledge of the Resistance is far too sensitive for him to risk capture by the Combine, and Alyx promises that she and Gordon will go after Dr. Mossman. After a call from an irritated Dr. Magnusson, Dr. Kleiner leaves to assist him in the final preparation for the launch of the rocket. As the G-Man appears on the screen behind her, Alyx delivers his message to Eli: "Prepare for unforeseen consequences." Upon hearing this, a shocked Eli nearly collapses and, in private, informs Gordon that the G-Man spoke those same words to him just before the Black Mesa Incident. Eli expresses regret for not aborting the test that led to the Incident and over the G-Man's present influence over Alyx.
They are soon interrupted, however, as they are informed a larger force of Combine advancing on the base, complete with Striders and Hunters. Dr. Magnusson introduces Gordon to the Magnusson Device, a sticky bomb designed to destroy Striders, and informs Gordon that keeping the Striders away from the silo is crucial, as a single Strider could destroy the rocket. Using the Gravity Gun to launch the devices, Gordon manages to defeat the attack force in the valley around the base.
 Chapter 7: T-Minus One
Alyx and Eli watch as the superportal is shut.
Eli begs Gordon and Alyx to destroy the Borealis
shortly before dying.
After the Striders are dispatched, Gordon returns to the Base and receives an unexpected thanks from Magnusson. Before the rocket launch and out of Alyx's earshot, Eli tells Gordon that he believes The G-Man's message is a warning regarding the Borealis, telling Gordon to destroy it and promises to elaborate further. He then tells Gordon that he is very proud and thankful of him, saying he "couldn't be prouder of you even if you were my own son". The rocket is then successfully launched, closing the superportal and preventing the Combine from calling in reinforcements from their homeworld. Alyx reveals that she found and fixed up an old helicopter that they can use to fly to the Borealis.
As Gordon and Alyx prepare to depart to search for Dr. Mossman, Advisors attack the helicopter hangar. They telekinetically pin Alyx and Gordon to the wall and seize Eli. Eli warns them both that the Borealis must be destroyed and then tells Alyx he loves her and to look away as the Advisors proceed to kill him, probing his mind in the process. Dog arrives and fights off the Advisors, forcing them to escape the hangar and freeing Gordon and Alyx from their control. After they fall to the floor, Alyx runs to her father's side and holds onto his lifeless body. As Alyx cries over Eli, the screen fades to black and the credits roll.