13 years later, the next installment in the Half-Life series is finally here. The VR-exclusive prequel to Half-Life 2 may not be what players expected, but it is nonetheless a worthy addition to the franchise and, surprisingly, sets up the future of Half-Life in a big way.
In Half-Life: Alyx, Alyx's journey takes her to a floating Combine facility known as The Vault where Eli believes a superweapon is being held. In the final hours of the game, the truth about The Vault is revealed and an important new character is introduced. The ending is a huge surprise and catches things up to the cliffhanger at the end of Half-Life 2: Episode 2.
Warning: Spoilers ahead for Half-Life: Alyx (obviously)
The "Scientist" And The Superweapon
Alyx is guided by her father to the vault to destroy whatever superweapon the Combine are protecting within it. Towards the end of the game, Alyx stumbles upon a woman having a conversation telepathically with the Combine about the Vault. Eli was wrong, it isn't a superweapon being kept in the Vault: it's a person, and it's someone that survived the Black Mesa incident in the original Half-Life. Obviously, Eli believes she must be talking about Gordon Freeman, so the mission continues as planned and Alyx pushes forward to free the savior of humanity from The Vault. But who is this mysterious woman?
While one may assume the voice belongs to Dr. Judith Mossman, Half-Life 2's traitor that eventually turns against Dr. Breen, the character is credited only as "Scientist". Usgamer.net spoke to the writer of Alyx, Erik Wolpaw, who explained that the Scientist is a new character they aren't ready to talk about, but they have big plans for her.
Changing The Future
Eventually, Alyx assaults the Vault and frees Gordon from his prison, or so she thinks. The Combine's prisoner is actually the enigmatic G-Man. The G-Man is an interdimensional bureaucrat responsible for many, if not all of the major events in the series. Upon being freed, he offers to grant a wish for Alyx. She asks for the Combine to leave Earth, but the G-Man explains that it's too big of an ask, and would be counter to the agenda of his employers. Instead, the G-Man offers Alyx an opportunity to save her father. He then teleports her to the final moment of Half-Life 2: Episode 2.
At the end of Half-Life 2: Episode 2, after launching the rocket to close the super portal, Eli Vance is unceremoniously killed by a Combine Advisor. That's where Episode 2 ends and where the series has remained for the last 13 years. The G-Man gives Alyx the chance to save Eli using her suped-up Russell gloves.
Unforeseen Consequences
After killing the Advisor, G-man tells Alyx that she has proven her worth to his employers and that she will now need to replace Gordon as their human errand-runner. Alyx protests, but the G-Man simply informs her that she doesn't understand the situation she is in, citing unforeseen consequences.
After the credits, Eli is indeed alive in the future, but Alyx has disappeared. Eli curses the G-Man's unforeseen consequences and tells the player, now Gordon, that they have work to do. He then hands the player Gordon's trusty crowbar.
"Unforeseen Consequences" has been a theme throughout the series. In fact, Chapter 3 of the original Half-Life is titled Unforeseen Consequences. During Episode 2 while the Vortigants heal Alyx, the G-man appears and whispers the phrase in her ear, instructing her to say the words to Eli when she wakes up.
She does, and Eli nearly has a heart attack. He explains to Gordon that the G-man delivered the sample to Black Mesa that caused the incident in the original Half-Life, and that when he delivered it, he whispered the phrase "Unforeseen Consequences" to him. It was assumed that the consequences were meant to be Eli's death, but the phrase has taken on an entirely new meaning at the end of Alyx.
The Future Of Half-Life
Before the Advisors attacked at the end of Episode 2, the plan was to board the helicopter and find Dr. Mossman before starting a new mission to locate Borealis. Borealis is an abandoned project by Aperture Science that would have seen the development of something like the portal gun on a massive scale. Eli fears that Borealis can be used to re-open the portal and flood the earth with Combine, so getting to Borealis first is imperative.
It was always suspected that Episode 3/Half-Life 3 would take Gordon to Aperture and bridge the worlds of Half-Life and Portal together. With Alyx seemingly out of the equation (for now) and Eli handing Gordon his crowbar, it's strongly applied that the next installment will return players to the role of Gordon Freeman. Whether that game will be another VR title or not is unknown, but what seems likely is a showdown between Gordon and Alyx, orchestrated by the G-Man, with Eli between them.