Story

Preface

Axiom Verge lays out its events through cutscenes and Notes hidden around the game. These often hint at actuality, but are sometimes ambiguous. Thus, there are many ways to interpret the game's story. In fact, this is the main foundation of the game: to question "What is real?" Below is one interpretation of Axiom Verge's story.

Story Synopsis

Many thanks to MrBeens on the GameFAQs forums for laying out the basis for this synospsis.

Trace is a scientist on Earth who works in a laboratory when a frozen pressure valve causes an explosion. Trace is severely injured in the explosion. For months, he is bedridden, blind, and paralyzed from the waist down. With little other stimuli, his mind turns to physics and the mysteries of the universe.

One day, Trace has an 'Epiphany that changes what we know about the laws of physics'. He begins publishing his theories, but the scientific community is skeptical of this drastic departure from established science. They blacklist him and start calling him 'Athetos' (derived from a Greek word), taken to mean 'without place', 'to do away with', or 'to reject'.

Using his new understandings of physics, Trace is able to cross 'The Breach', which is a barrier between worlds. Crossing the breach, he finds the world of Sudra. Sudra is a gateway world of sorts—its purpose is to regulate travel between other surrounding worlds. However, by the time Trace arrives, Sudra's civilization has collapsed, and its inhabitants no longer remember that purpose. They have become an incredibly xenophobic society and shunning all outsiders, and regarding their own technology with superstition and religious reverence. The Sudrans no longer permit travel between worlds. They see the Breach as a barrier to shut them off from all the outside universe.

Upon his arrival, Trace is still in a wheelchair, but discovers Sudra's incredible technology and uses a 'Re-Birth' chamber to completely heal himself. This chamber is one of the egg-shaped save points in the game. By using this chamber, he also inadvertently leaves behind an imprint of himself. This same chamber, years later, will be the starting point of events of Axiom Verge.

For some time, Trace explores Sudra and makes contact with its inhabitants. Trace eventually decides the Sudran technology is too dangerous to bring back to Earth, believing it is connected to the catastrophic collapse of Sudra's civilization. He then attempts to go "upstream - to the Filter, or whatever lies beyond - for answers."

In doing so, Trace discovers that there is a world beyond Sudra—one with an incredibly advanced civilization that the Sudran's have kept hidden due to religious taboo. This world is full of technological wonders that could end all war, strife, and sickness on Earth. Athetos decides that the needs of the many outweigh the needs of the few, and that the only way to bring this technology back to Earth means destroying the Sudrans, who would refuse passage between Earth and the world beyond. So, he begins creating allies—genetically modified or "variant" clones of himself, using the imprints he has left in the Re-Birth chambers. He wins also convinces Kraskinki, one of the Rusalki (giant war machines that guard Sudra), to aid his cause. Feeling secure in his army, Athetos goes on the offensive with biological warfare, creating a pathogen that wipes out the Sudrans almost entirely.

The only thing that would stop him now are the three remaining Russalki— Elsenova, Ophielia and Veruska, who stayed true to their purpose of guarding Sudra. They battled against Athetos, his variants, and Kraskinki. Using Remote Drones, they manage to destroy Kraskinki and Athetos's mobile pathogen protection, forcing Athetos to retreat to a hideaway in Mar-Uru, far above the surface of Sudra. However before he does so, Athetos manages to turn off the Remote Drones, leaving the Rusalki nearly helpless, dormant, and degrading.

Since they cannot stop Athetos in this state, Ophelia comes up with a new plan. She will create a new copy of Trace, from his imprint when he first was healed, back when he first came to Sudra. Though it has been a long time, the Rusalki are aware that Trace was much kinder when he first arrived on Sudra, they theorize that using this imprint will produce a copy that will be more amenable to the idea of stopping Athetos.

This is where the playable events of Axiom Verge begin. The copy of the younger Trace is the player throughout the game, and by re-activating the Remote Drones, he is able to repair Elsenova to her more mobile state. Then, he finds Athetos in his hideaway above Sudra, and during the battle, momentarily disrupts the Breach Attractor, allowing Elsenova to come help destroy it entirely. After doing so, the Rusalki are once again free to move about above the planet's surface, and Elsenova chooses to kill Athetos. Once that is done, Elsenova sends the copy of Trace back through time to the point of the lab accident aftermath, altering history so that the event does not leave him injured...or so it appears.

"Back in time", Trace cannot stop thinking about Sudra, and devotes his life to returning. In the final cutscenes, he is near to his goal of returning, and we see a brief glint in his eye, indicating that he may be on the path of becoming Athetos once again.

...

But that's not really the end, is it? If you complete the game with a high percentage of items, you'll be treated to two important bits of information. First, watching the full credits shows a collapsed Trace, laying at what appears to be the base of a Rusalki body. Second, back on Earth, when Trace nears his goal of returning to Sudra, Athetos seemingly pays him a visit! Athetos tells Trace he cannot outrun himself; he tells him that it is "time to wake up" and then shoots him!

If you think about it, there's nothing in the game to imply that Elsenova can send Trace back through time. After defeating Athetos, Trace asks her how he can go back to Earth as a mass-murderer, to which Elsenova replies that he needs not worry—they have "taken care of it". What we do know, is that Elsenova is able to subdue the clone of Trace at will, killing him, or in this case putting him into a coma. Trace going back in time to the point of the lab accident is all a dream, contrived by the Rusalki to give Trace a happy state of being, but at the same time preventing any possibility that he might once again become Athetos...or so they think. In this coma, Trace's mind realizes what is happening, that his world is not real, and so it creates a "kick" that will wake him—Athetos coming to kill Trace.

Alternate Story Interpretations

This section will contain any alternate interpretations to Axiom Verge's plot. Alternate interpretations are those that do not take the game's events "at face value", and instead, seek to read the subtext to define what really happened.

What if it was the Rusalki, not Athetos, who released the Pathogen?

Consider that the Rusalki are upset ("bitter") with the Sudran people (see "The Storm" Note). The Sudrans activated the Breach Attractor to shield their world from the rest of the universe, and in doing so they trapped the Rusalki on Sudra. Being trapped beneath the planet's surface seems to have detrimental effects on the Rusalki's health, as there is the notable death of Oracca.

First of all, we know that Trace is lied to throughout most of the game. So, we cannot take what either Elsenova or Athetos says at face-value. The Notes throughout the game provide more reliable information, and it's necessary to interpret the subtext.

This theory answers several questions that otherwise seem to be plot holes...

• Why would Athetos and the Rusalki become enemies in the first place? They both want the Breach Attractor turned off, and they both have a bone to pick with the Sudrans. Unless they don't. Maybe the Rusalki, upset at the death of one of their own, decided to unleash the Pathogen on the Sudrans, and Athetos is actually trying to stop them.
• Why does the Note "Athetos" say that Katrahaska "got to" Athetos "before I had a chance"? If she had sided with Athetos to kill the Sudrans, then why would the other Rusalki care if she contacted him? Unless, Katrahaska "siding" with Athetos meant she was actually against releasing the Pathogen, and warned Athetos in the hopes he could help stop the Rusalki.
• Why does Athetos say he 'can't tell Trace everything, or his captors would kill him (Trace)'? Athetos may know that if he reveals the truth right away, the Rusalki will have to kill Trace, else he would side with Athetos. Instead, he goes along with the lie, but gives Trace a reason to believe Athetos is benevolent, and hopes Trace will be able to stop the Rusalki where he has failed.
• Why would Athetos develop a biological pathogen, that seemingly has no effect on the Rusalki. The Rusalki are certainly a much greater threat to him than the Sudran people. It would make more sense that if Athetos struck first, he would take out the Rusalki, and then kill the Sudrans...not the other way around.

There is a single note called "Security Notice" that states "The intruder who commandeered the storm talisman is suspected of releasing a plague." But who has raised such a suspicion? It's possible the Rusalki used Athetos as a convenient scape-goat, to misdirect the Sudrans into believing that he was responsible for the Pathogen.