WARNING, SPOILERS AHEAD. This chapter discusses material covered later in the project.
The first narrative chapter focusing on Natasha Alexander (and how she came to be in command of Department Sigma) can be found here.
Dust to Dust:
Bester: It's hard getting used to the silence.
Garibaldi: What silence?
Bester: Even when a telepath isn't scanning, you pick up a constant background hum, like voices just beyond what you can hear. It's always there. The sleepers turn it right off. It's a strange feeling. Like walking with one of your eyes closed. So quiet.
Garibaldi: Oh, great. Maybe it'll help your insomnia.
Bester: Unnecessary. I sleep peacefully and contentedly. The sleep of the just.
Garibaldi: Maybe the just might have a few things to say about that, huh?
Bester: Okay, that's enough. You don't like me any more than the captain or Ivanova, that's fine. But get this straight: My blood is the same color as yours. And what I do, I do to protect Earth, same as you. You don't like how I do it, that's your prerogative. But there are things going on out there that you know nothing about, threats to the human race that no one ever hears about because we stop them. There's dangers all around us. And whether you like us or not, we may be all that stands between you and the abyss.
Around 2148 or so, as humans began to explore Mars, they dug up some strange alien artifacts (later determined to be of Vorlon origin). The company that would one day become IPX as we know it found some of the first artifacts and brought them to Earth. They hired a telepath, Mr. Raskov, to scan them, and discovered that the artifacts were somehow alive, sort of... whatever they were made of, they produced a telepathic effect.
Though the artifacts were technically property of the Earth Alliance (and housed in the US), IPX began a secret series of negotiations to try to sell them "under the table" outside the US, for the highest price, and plotted an insider trading scheme to profit off the disclosure of the artifacts' existence. Mr. Raskov, now brought back for these negotiations, wasn't down with it, so IPX ordered his murder to cover their tracks. Psi Corps was already aware of the existence of the artifacts - the subsequent investigation into Mr. Raskov's death led to the Corps' confiscation of the artifacts.
And not a moment too soon, because the IPX labs, and the government vault that housed them, were both located in San Diego, and the city was nuked by terrorists in a few years time.
At first the Earth Alliance denied the existence of the artifacts, but in 2156, the Centauri landed, and then everyone knew alien civilizations existed. With humanity formally in contact with another race, EarthGov publicly admitted that the artifacts had once existed, but declared that they had been destroyed along with the rest of San Diego.
In 2173, on Mars (Syria Planum), Psi Corps built a secret research facility to study the artifacts. They code-named the base "Department Sigma." And for almost two decades, Department Sigma's mission was purely that - to study the Vorlon artifacts of Mars.
Their mission eventually became much, much more.
In 2189, Kevin Vacit, and his then-aide Natasha Alexander (Lyta's grandmother) were both taken aboard a Vorlon ship. That Vorlon delivered to them both a personal message - it told them of the Shadows, of the great war that had once taken place between the Vorlons and the Shadows, and of the Shadows' plan to destroy humanity. It told them of the unique role telepaths would play in this upcoming war, and impressed upon them the importance of their destiny.
Kevin and Natasha didn't speak much of this encounter for several years, but as Kevin aged, and he realized his time in this world was drawing short, he worried about who the Senate would choose to replace him - no doubt that man or woman would be a normal (unlike Kevin, who was secretly a telepath), and no doubt he or she would have a very different vision of the Corps. He called Natasha to his side and appointed her to command Department Sigma, which, he decided, had to expand its mission and scope.
The Vorlons, indeed, had "tinkered" with the human genome to produce more telepaths than had previously existed in the population, and telepaths of greater strength than had existed before. But Crawford's incitement to violence against telepaths, in 2115 and later, had led to the murder of many telepaths (and normals who carried the genetic marker). Additionally, an untold number of babies who would have grown up to be telepaths (or the ancestors of telepaths) had been aborted in the womb.
Such was the consequence of anti-telepath incitement: there were (probably) far fewer telepaths alive than the Vorlons had planned.
No one could know when the Shadows would arrive, how much "margin of error" the Vorlons had calculated, or how many telepaths would be "necessary" to defeat the threat, but Kevin and Natasha knew that the slaughter of so many telepaths so early on could easily spell disaster for the human race. Even the rules against intermarriage between normals and telepaths, and the genetic matching programs between telepath partners (programs instituted under Crawford and fostered by Vacit) weren't enough to make up for this gap - the Shadows could arrive any day. Humanity needed some way to make telepaths stronger, and to make more telepaths - immediately.
Department Sigma's mission expanded to address this new realization. Natasha's mission was to accelerate the study of alien artifacts, and using reverse-engineered Vorlon technology, to develop any and all means necessary to fight the Shadows. Department Sigma needed drugs that could make telepaths stronger, even push past P12. (Kevin Vacit, himself, was higher than P12, so he knew it was possible.) They needed drugs that could enhance rare telekinetic abilities, and drugs that could tie into latent genes and trigger telepathy in normals (because in a pinch, these people might be needed to defeat the Shadows). They needed warships. They needed pilots. And they needed to do it all in secret. EarthGov didn't yet know about the Shadows, and the Corps wanted to keep it that way.
When Director Johnston came to power around 2202, he began a purge of all telepaths in the Corps who had once been close to Vacit, and of anyone who challenged him or opposed him in any way. His Corps would be run entirely by him, with an iron fist - not by the telepaths in it. One by one he trumped up charges against all of Vacit's former aids and colleagues, and had them executed or exiled. Natasha (who had been closest to Vacit) was, for the moment, safe on Mars.
Perhaps you have have noticed something curious about the Black Omegas - they exist. Earth banned telepaths from military service, but Bester's squadron of Black Omegas is an official Earth Alliance squadron, formally attached to Psi Corps ("This is Earth Alliance Squadron Black Omega to stolen transport. Surrender and prepare to be boarded."). The "Black Omega" model starfuries are also the most expensive, sophisticated model of starfury. Why would Earth give the Corps these sophisticated ships, and let telepaths train pilots and elite bloodhound commandos to fly them, if they wanted to keep telepaths from wielding any real military power? Sure, ostensibly the Corps has these ships to track down and detain off-world rogues, and yes, they do use them for that purpose, but what's the real origin of these ships? How did Bester really get command of this squadron?
The answer partially involves Department Sigma, but we'll discuss this later in the project.
At some point between around 2240 and 2256 (canon doesn't specify, but it was probably after the Earth-Minbari War), Johnston did catch up with Natasha and have her assassinated. Now a part of the conspiracy with Clark and the Shadows, Johnston and his people attempted to take over Sigma and shut down their programs. To resist, Sigma had to conduct their research even more in secrecy, and had to disguise the true nature of their work. For instance, they told Johnston that the "stable telekinetic program" (in which Ironheart eventually participated) was really to produce elite assassins for him.
Sigma had had some mishaps, as well. The drugs Sigma developed to tie into latent genes and make normals telepathic never worked the way it was intended - it was highly addictive, and made people highly violent. In the late 2230s or early 2240s, one of their scientists, realizing the drug could make him or some quick money on the black market, went "rogue" from the lab, stole Dust and the process to make it, and started selling it on Mars and off-world (e.g. on Europa). Sigma panicked, and called Bester. (Natasha had met and briefly worked with him years before, during the Black Fox raid, and she held him in great respect because he, too, had once been close to Director Vacit.) By the time Bester caught up with the rogue scientist, it was too late to contain Dust - the cat was out of the bag. (Bester, as he says in Dust to Dust, always thought the whole Dust program was a mistake.)
EarthGov never knew for sure who had cooked the stuff up, though they swiftly made the "new" drug illegal after seeing its dangerous effects. They managed to contain the problem to off-world, but it became an intractable problem on crime-riddled colonies such as Europa.
Even with the failure of Dust, Sigma continued their work on the other projects. To conduct their research on the neurological workings of telepathy (and how to tinker with it), Sigma worked on human subjects. These subjects, as far as I can tell, were all volunteers, and they all went into the program knowing they might not come out, and agreeing (eventually) to donate their bodies to Department Sigma for study. Jason Ironheart, for instance, a P10 and Psi Corps instructor on Mars, volunteered for the experiment of which he was a part.
Canon distorts and misrepresents the nature of the human subjects research in which Sigma was engaged, attempting to vaguely link it to Nazi-era experiments on Jews. While it is true that Sigma did dissect the bodies of some of its subjects, Sigma's research subjects were volunteers. They were, by and large, the Corps' most loyal and devoted patriots, who sacrificed their well-being (and at times, their lives) so Earth could have an effective defense against the invasion of the Shadows.
As the vision of G'Kar's father says to him in Dust to Dust, as Bester says to the other Psi Cop in the shuttle at the end of the same episode, and as Delenn says to G'Kar in Ship of Tears (in regards to the sacrifice of Narn lives so the Shadows don't know the other races are aware yet of their movements): We are fighting to save one another and some must be sacrificed, if all are to be saved. These brave telepaths understood this principle, and sacrificed themselves to save Earth, in no less heroic a fashion than normals died in the Battle of the Line.
Bester himself volunteered for a Sigma experiment. He volunteered to be injected with a human-engineered virus that would affect the neurological systems in his brain that control telepathy, so that Sigma could better study and understand these systems in high-level telepaths. In his case, the experiment had no permanent effect as long as he regularly took a medication to suppress the virus (but for him not to take the medication every two weeks would be very dangerous). (He didn't get infected with this virus "accidentally" or by someone "out of revenge," as Garibaldi speculates in Final Reckoning - he volunteered. And as horrified as Lyta is that Bester asks her to sign a form promising her remains to the Corps when she dies, he signed such a contract himself. To him, it's what any reasonable telepath would do if, after death, he or she could still contribute to the betterment of his/her people in some small way.)
What Ironheart says about the "true purpose" of the program (and the Corps in general) is entirely untrue (and in a creepy twist, actually plays on the anti-Semitic tropes of a World Zionist Conspiracy simultaneously as it implies, as canon does elsewhere, that the Corps = Nazis). It's not clear whether he mistook what Sigma told Johnston (and York) to be the truth of the program, or whether he simply went mad, but there is no factual basis to his supposed "revelations" about the Corps and Department Sigma's plans ("The Psi Corps is dedicated to one thing, commander. Control. Control over telepaths, the economy, the courts. Over matter, over thought itself." WORLD DOMINATION!).
(How he turned into a being of pure energy and flew away, however, is a complete mystery to everyone, including Bester and everyone in Department Sigma! And me, too.)
When Ironheart killed a researcher at Sigma, stole a ship and fled the lab on Mars, Sigma again called Bester. That is how Bester first ended up on the Babylon 5 station - Sigma informed him that in a matter of a couple days, Ironheart might have the telekinetic strength to destroy the station, he was losing control, and could do it by accident. That station had 250,000 humans and aliens on it. Bester and Kelsey went to Babylon 5 to apprehend Ironheart and save everyone's asses.
But they couldn't tell the command staff anything about the true purpose of the program Ironheart was involved in, because the command staff knew nothing about the Shadows - and Sigma had to keep its programs to fight the Shadows under the tightest secrecy, lest the agents of the Shadows, embedded in EarthGov, learn of their plans. (It was preferable for the command staff to think the Corps is a bunch of Nazis than for Bester to risk those Shadow agents learning the truth - and it would even have been preferable to lose the station than to blow the cover on the secret program and put all of humanity at risk. As Bester says, "a calculated risk." In his line of work, everything is a calculated risk.)
Now, there is one more point to be made, and that concerns the events of Soul Mates. Bless his heart, but Peter David just kind of made that one up. :) Don't get me wrong: In general, I love Peter David's work. He was my favorite author when I was in middle school - I read some of his books over and over again. He has written some material that I love dearly. But he missed the mark on that episode. I can only speculate as to what happened, and I'm not going to do that here (and to a large extent, I think much of the relevant canon hadn't been written yet, so he was working with limited material). But with heavy heart I have to declare much of that episode (at least as concerns human telepaths and the Corps) to be canon error. Telepaths are able to pick up on both emotions as well as thoughts (as Talia, Lyta and others mention throughout canon) - there is no separate class in Babylon 5 canon called "empaths," like Star Trek's Deanna Troi. A telepath who ceases to be telepathic (say, through stroke or injury) doesn't just "leave the Corps." (I can't imagine the Corps would do this to their own people in the face of a grave disability that prevented them from legally working!) The Corps wasn't doing secret experiments that could result in someone losing telepathic function - they were working to achieve the exact opposite. And being an "empath" doesn't make one an abusive, emotionally manipulative person. (Though her ex-husband could have been so before, which may have been why he and Talia divorced!)