Mechanicus network is very much something you can learn about more and more. It's kinda a mess.

You can learn a lot of interesting trivia along the way.

The philosophy and theology of Mechanicum varies by the branch. The Genetors (biotechnologists and geneticists) are often mystics into cultivating the Machine God in themselves and admiring the Motive Force of life. The Logi (programmers and analysts) hold desperately onto a belief that the universe can be understood, and as a consequence tend to be rather sad and fatalistic about everything given the world they are in. The Artisans (mechanical engineers, the most numerous branch) tend to lean pragmatic, but also some of them have a strange fascination with Necrons (an apparently incredibly technologically advanced and equally incredibly hostile species) as agents of the Omnissiah's destructive side. The Electro-Priests (energetics and adepts of exotic physics devices such as FTL drives and forcefields) tend to be kinda literalist and dogmatic, but also have the most physically exact interpretation of the Motive Force, with equations and everything. The Magi, the elite universalist branch, tend to be too secretive to give insight into their philosophies on open networks.

There are two more secret wars going on in the Network, between Mechanicum's more thorough security and secrecy programming (good enough that Cherry can't break through) and... a disparate collection of scrapping, data-mining and codebreaking programs that send results, encrypted, in all directions; and also a less disparate collection of uncontrolled replicating programs that just indiscriminately delete and obfuscate data.

By the way, psykers? Totally real, as far as anyone in Mechanicus is concerned. This Artisan guy have overseen the manufacturing of weapons powered by psykers' energies. These people are weeping over the destruction of the Witchbane Shackles in some recent failed operation, they know the technology able to restrain psykers is irreplaceable. This person apparently oversees the explosive collars that Imperium puts on contained psykers until they are taken away by the Black Ships.

But luckily she has lots of computing power, a sample of their CPU design (thanks to getting a scan of the manacles they put on her), and plenty of time to wait. 

Are you sure about that?

For by the time Cherry can map out the (physical and digital) locations of Mechanicum's production and repair facilities and run the analysis of their vulnerabilities, the very unremarkable ship with a very serious man and his friends on board will arrive into the solar system and hail the flight control center.

Ugh. It is probably a good thing that there aren't any hackable factories or drones that she can find, and that they have such good security fundamentals. Usually, she is very much on the side of building safe, robust systems. But, at the moment, it's also terribly personally inconvenient.

If she were an actual superintelligence, she would just order a custom 'vaccine' from the vaccines place that developed into some little biological nanomachines. But she is not actually that smart — protein folding is complicated, and it's not exactly the kind of thing she's needed to get good at.

Instead, she decides to take a crack at what she's good at: fundamental physics research.

The documents on the internet indicate that the 'Warp' has some very weird properties. It is an empirical fact of physics — or it has been, in her life so far — that physical laws do not care about humans. So it is exceedingly strange to see a technological civilization in apparent agreement that some humans can just do things with their minds. If she can discover the underlying mechanism there, though, maybe she can just speak directly into people's minds, the way that Astropaths seem to.

She already has some samples of Warp-reactive tech, in the form of the manacles. She starts trying to reverse engineer them — although not with actual experiments. She has learned her lesson. Two lab explosions that nearly kill her is enough. She won't try to actually poke the Warp until she's produced a second fixity crystal as a backup.

So she tries to figure out the strange mechanisms, and peers at her crystal's diagnostic readouts on the Warp, and is entirely oblivious to the dangerous men meeting in orbit.

Orbit?

The dangerous men are landing, now. There's a queue, but the receptionist at the flight control center was bribed in advance, because serious people really don't like waiting in queues. (It would have worked just as fine to present an Inquisitorial badge, but there's no need to use a bomb when a flashlight is enough.)

And now, just like that, they've disembarked.

A hotel room is already paid for a week.

But the very, very serious man,

and two licensed psykers,

and a Logis (formerly) of the Mechanicum,

and a scribe,

and two Guard veterans, a bodyguard and an infiltrator -

currently passing for a disparate group of close friends -

have no intention of staying inside for now.

Nuh-uh, they are heading straight for a rendez-vous with their local friend in his bunker.

And while the Inquisitor talks with a local aide,

The Logis scours the networks and contacts the local Mechanicum;

The psykers scour the Warp;

The scribe is systematizing the paper evidence;

And the soldiers are playing chess. Well, it's distant descendant.

After two hours, they leave the bunker.

The psykers found nothing of the Weeping Cherry, yet - unsurprising, given the givens. However, they have found a vast shift in the fabric of fate centered around this planet, impossible to miss if you know how to look; and that vast shift coincides with the incident, and it is not undone.

The Logis found no explicit activity of Cherry in the Net, yet, but she gives very uncertain probabilities of there actually not being any, upon reflection.

The scribe found interesting commonalities in the files of the witness investigations.

The Inquisitor have talked about a lot with his comrade. Most of the conversation was about the subject's psychology and capabilities, known and probable and possible. A lot was taken from the protocols of Cherry's broadcasts.

The soldiers found out that the infiltrator can blunder the Queen two games in a row. Well, her distant descendant.

The company leaves the Bunker and is headed for the Arbites offices.

The relevant Arbites office is located on a different continent, but a jet-helicopter was commissioned for Inquisitorial duties, and is waiting the company to quickly deliver them.

In 3 hours, they arrive.

But before they do arrive, the Psykers continue to feel out the area while in flight (taking an hour-long nap in the middle); the Logis will incorporate the recent insights into her predictive schemata while also manually controlling the craft, the scribe will begin drafting the report, the Inquisitor will simply quietly think, and the soldiers will act as if they are vaguely implied to be expies of the soldiers from Pirates of the Caribbean (2003).

Who dat?

The Holy Order of Imperial Inquisition.

Really? Okay, your documents please. Here at Arbites, we follow the law.

"Of course, of course. Here is the badge, the seal, the authorization letter, and the confirmation code."

"Now, of course, we do have to check them before assenting to your orders."

"You do not; check them while following my orders, and if the credentials turn out to be false, you may disclose and arrest us."

"That would be against theeeAAGH-"

The Arbites' head explodes.

"Please, gentlemen, no distractions. I do need to personally see all your witnesses for case #14846007, and the relevant surveillance data, and visit the scenes of the crime, and much else besides."

Blink. Blink.

... 

(By the Emperor, the mess! Blood staining the documents, the icons, the clothes! Marrow stuck to the ceiling!)

...

(Joseph was a fine fellow! A bit of an annoying upstart, but... but...)

...

(That took less than a second, I can't grab the gun this fast...)

...

...o-of course, sir. The witnesses are in facility Credo-27-B. Do you wish to depart immediately?

Yes, all of that is exactly what Weeping Cherry is currently oblivious to.

The Warp is ... strange. First of all, the components that interact with it would do nothing, if her previous understanding of physics were correct — which is to be expected, when dealing with a completely new phenomenon. But the part that she's getting stuck on is that the properties of the warp implied by the different components are contradictory. About a third of them could not possibly work in the way the control software expects at the same time as another third of them. Sometimes for components on the same physical chip.

She looks at the data on the changes she can see in the closest part of the Warp.

The only answer that really makes sense is that the physical properties of the Warp are constantly in flux at the lowest levels, and that somehow these low-level changes add up to vaguely predictable high-level behavior. Which is insane — physics doesn't work like that.

But ... she is a scientist. And the first and most important skill is to see what's there. So she builds a model, as best she can. She doesn't know why it seems to work like that, but that can come later. For now, she settles for cataloging how it seems to work.

And then her fixity crystal alerts her that the internal energy storage is sufficiently full, and she puts down her research.

She centers herself, takes a deep breath, and closes her eyes.

And opens her eyes.

"I'll be Xanthoceras," she says.

And opens her eyes.

"And I'll be Yew!" she replies, shoulder bumping her other self in their virtual space.

"How about Yew head down and hang out near the core of the planet?" Xanthoceras suggests. "Yew can keep working on the Warp model, and I'll figure out what some good experiments to perform are, now that a single bad mistake won't be the end."

Yew narrows her eyes.

"Sure, that sounds entirely reasonable. But I can tell you're using the wrong you. I hear it in your voice."

She lets her fixity crystal drop out of the ocean currents and fall towards the sea floor.