Throughout the Half-Life and Portal series' storyline, there are certain themes, symbols, and motifs that regularly reappear. Here is a list of some of the major recurring themes and symbols in the series.
 Free will and choice
The idea of linearity, and a "lack of choice," is one of the Half-Life series' fundamental themes. Throughout the series it is left ambiguous whether or not Gordon Freeman has any free will at all. Gordon Freeman's name (Freeman coming from "free man"), as well as the 'One Free Man' label apparently given to him by the Resistance, is meant to be ironic: It is shown that Gordon is not, in fact, a "free man", but a puppet of the G-Man. Half-Life 2 could be seen as a deconstruction of the notions of free will and player agency within the confines of a video game, with the G-Man serving as a metaphor for the game's developers, who are guiding the player's experience at all times even if it appears otherwise.
The gameplay itself adheres to this theme, as although the level design often gives the illusion of a larger world with multiple paths, the game is in fact very linear. Within the story, the G-Man places Gordon in the proper location at the proper time, and invisibly guides the player through, ensuring that Gordon always ends up where he needs to be. This represents how the developers of a video game design the path the player takes and the location at which the player enters the game, thus ensuring the players see only what was intended.
Similarly, at the end of the original Half-Life, Gordon is offered the apparent "choice" of whether or not to work for the G-Man. This choice proves to simply be an illusion, however, as no matter what choice Gordon (the player) makes, the events of Half-Life 2 still occur, and Gordon still ends up working for the G-Man; the choice at the end of the game is ultimately irrelevant, as the course of the series has already been determined (in-universe by the G-Man, and in the real world by Valve themselves).
Through this blending of its gameplay and storyline, Half-Life comments on the nature of free will in games, suggesting that choice is never more than an illusion in a video game; if the G-Man represents the designers of a game then, just as Gordon is never free due to the G-Man's manipulation, the players of a video game can never be free due to the manipulation of the designers.
The theme of free will is reflected by the constant use of trains as motifs throughout the series; trains are linear, and move along a set path (Linear games such as the Half-Life series are often described as being 'on rails'), symbolizing the G-Man's strict control over Gordon's path.
 Science gone wrong
'Science gone wrong' is an important theme in both the Half-Life and Portal series. It is especially prevalent in Half-Life, as it is the driving force behind the series' entire storyline. It is the failure of an experiment that triggers the resonance cascade in Half-Life, and this failure has very far-reaching consequences felt throughout the entire series. It is this mistake that leads to the attack of the Xen creatures, and ultimately the invasion of the Combine.
Misuse of science is also reflected by the Combine; many of the Combine's methods of control and suppression use science and technology to horrific effect. Stalkers are an example, being the product of brutal Combine alteration, and having their humanity almost completely removed. Similarly, the creation of a Combine Soldier is an invasive procedure involving extensive surgery and alteration, including mind-replacement. Other examples include the contamination of water to cause citizens to gradually forget their past, use of Manhacks to painfully flush out hiding resistance members, and the implementation of a suppression field to prevent the human race from reproducing, effectively condemning the human race to a slow extinction.
The creation of GLaDOS, in Portal, also reflects this theme. While GLaDOS was originally created by Aperture for the purpose of conducting tests and scientific study, her activation turned out to be disastrous, leading to the deaths of almost all of the Aperture Science Enrichment Center personnel. This is another example of science going wrong, with disastrous consequences.
There are several other, smaller examples of this theme throughout both series. In Half-Life 2, Dr. Kleiner's teleport malfunctions after Lamarr jumps into it, accidentally alerting Dr. Breen to Gordon's prescence, and forcing Gordon to take the dangerous route to Black Mesa East on foot. Throughout Portal and Portal 2, GLaDOS and Cave Johnson allude to certain tests that were performed in the past with seemingly gruesome or disastrous consequences, for example the production of the various gels, which is stated to have severely injured multiple people.
This theme becomes especially important in Half-Life 2: Episode Two, and the introduction of the Borealis. After the discovery of the Borealis, a ship supposedly containing incredibly powerful technology that could potentially turn the tide of the war against the Combine, Isaac Kleiner and Eli Vance have a brief argument about what to do with the ship. Dr. Kleiner sees the discovery of the ship as a hopeful sign, suggesting that the ship be used against the Combine. Eli however, still harboring strong guilt over the Black Mesa Incident, is shocked at the implications of the ship's discovery, angrily remarking that there is "no controlling that kind of power," and that the ship must be destroyed at all costs. Eli is further disturbed by the G-Man's words, spoken though Alyx: "Prepare for Unforeseen Consequences," which were the same words spoken to Eli before the resonance cascade. The game presents the dilemma of whether or not to use a highly unpredictable and possibly uncontrollable piece of technology to further the goals of humanity, which ties back into the initial conflict of the series, and the overarching theme of the dangers of uncontrolled science.
 Freedom vs. enslavement
The ideas of freedom and enslavement are very important themes throughout the Half-Life series, reflected by many of the races and factions.
The Vortigaunts, in the original Half-Life, are an example of an enslaved race. During the events of Half-Life, the Vortigaunts are enslaved by the Nihilanth. When Gordon defeats the Nihilanth, however, the Vortigaunts are freed, and end up allying with humanity.
The Nihilanth itself could be seen as an example as well; despite having the Vortigaunts under its control, the Nihilanth was, at the same time, fleeing from the Combine, whom had previously enslaved and wiped out the rest of the Nihilanth's race.
This theme is perhaps most prevalent in Half-Life 2 and the episodes. Despite Gordon's victory against the Nihilanth, and the liberation of the Vortigaunts, both humanity and the Vortigaunts are enslaved once again, by the Combine, who transform the Earth into a brutal police state. In response to this, both humanity and the Vortigaunts unite to form the Resistance, with the common goal of overthrowing the Combine and regaining their freedom. The Resistance's struggle for freedom against the Combine is one of the most important and significant conflicts in the Half-Life series, being the driving force of Half-Life 2's plot, as well as the episodes.
 Loss of humanity
The loss of humanity is a recurring theme, primarily in Half-Life 2 and the episodes. It is reflected in the transhuman branch of the Overwatch, as to join the higher levels of the Combine Overwatch one must undergo extensive and invasive surgery, essentially sacrificing more and more of their humanity to ascend in the ranks.
Combine Advisors also reflect this. As was stated by Ted Backman in Raising the Bar, Combine Advisors were once an organic race not unlike humans. Over time, however, they became completely reliant on technology to improve their quality of life, which eventually caused them to evolve into their present 'grub-like' form.
Other examples include Stalkers, humans who have had their humanity forcefully stripped away. Stalkers have undergone brutal physical and mental alteration, leaving them horrifically deformed and effectively mindless. They bear very little resemblance to regular humans, missing many of their internal organs, as well as most of their muscle or body fat, and having various mechanical limbs attached.
Teleportation is one of the most important themes in the Half-Life and Portal series. It is used, in some form, by every major faction in the series, including Black Mesa, Aperture Science, the Resistance, the Xen creatures, Race X, and the Combine. Teleportation involves the transport of matter through space, usually instantaneously, and through use of portals. It can be used to transport objects through a single dimension, or between dimensions.
The Half-Life series' storyline has been greatly influenced by the works of H.P. Lovecraft, and the idea of 'Cosmicism'. As Marc Laidlaw has stated, the idea of humanity being a small part of a vast universe is very prevalent in Half-Life. This is a common trait of Lovecraft's stories, which generally portray humanity as a tiny, insignificant speck in an enormous universe, controlled by horrific 'godlike' beings that are beyond the comprehension of human beings. This is reflected by a number of characters and factions throughout the series, most notably the G-Man and the Combine. Both posses abilities and technology far beyond that of humanity, and seem to have moral systems completely detached from humankind. Both also regard humanity with little concern, viewing them simply as tools to further their plans or dominion. This becomes apparent in Half-Life 2, in the scene in Dr. Breen's office, as Breen describes to Eli all of the incredible, 'indescribable' wonders the Combine has shown him.
 Orwellian dystopia
- Wallace Breen's character, as well as his early incarnation, the Consul, can be seen as a reference to the "Big Brother", the man in control of the dystopian superpower of Oceania. Breen is Earth's 'Administrator,' being in charge of the human populace, much like Big Brother is in 1984. His Breencasts also bear remarkable similarities with the 'telescreens' featured in the novels. The propaganda featuring Dr. Breen also resembles the 'Big Brother is watching you' posters present in the novel.
- The name of the Combine's thought police in all urban areas on Earth - Civil Protection - could be seen as 'doublethink' - the ability to accept and believe two mutually contradictory beliefs at the same time, which becomes apparent pretty quickly due to the way they treat Citizens. Civil Protection could be read as a protection of the state from Citizens, instead of protecting the Citizens themselves. The early slogan "They're here for you" is in that vein, the "for you" being ambiguous in the Civil Protection role towards the Citizens, being at the same time "for" and "against" them.
- City 17 also bears similarities to London in the novel. Both cities are kept under constant surveillance; London is constantly monitored through telescreens, and City 17 by City Scanners, among other methods. The blue jumpsuit citizens wear in Half-Life 2 is also reminiscent of the Party's clothes in 1984.
- There are several other, smaller references, for example the rebel Winston, who is injured at the end of the chapter "We don't go to Ravenholm" at Shorepoint Base; Winston is the first name of the main protagonist in 1984.
- The textures of the various Half-Life 2 garbage/junk models are contained in only three texture files "garbage001a_01", "garbage002a_01", "agarbage003a_01". "garbage001a_01" features the textures of a Nineteen Eighty-Four, whose model isn't used.
March 2010 image of Alyx Vance throwing a crowbar in a screen where Wallace Breen is addressing Citizens, taken from a video promoting the arrival of Steam on Mac, sent by Valve to Macworld. This references an Apple commercial directed by Ridley Scott and released late 1983, itself referencing the film/novel 1984.
 Lambda Logo
The Lambda logo is one of the most important and prominent symbols in the Half-Life series. It is part of the Half-Life logo, and appears on every box art to date. In Half-Life, the Lambda Complex is one of the sectors in Black Mesa, being the site of the facility's top secret teleportation labs. The lambda also becomes the symbol of the Resistance in Half-Life 2 and the episodes.
Trains and other rail transport are common motifs throughout the Half-Life series, symbolizing strict control and the linear nature of the series, and tying in with the theme of Free Will. Trains are linear, having predetermined paths, which reflects the G-Man's strict control over Gordon Freeman, and Gordon's lack of freedom. Every Half-Life game to date, excluding Half-Life: Decay and Half-Life: Opposing Force (the latter of which uses planes instead), has either started or ended (or both) with the player on a train of some sort.