The book titled "Emperor Pius Dei" isn't just a reference to Petey being a virtual god. Its initials are "PD." Also, "Pius Dei" translates approximately to "dutiful god." It's a mission statement.
What does Petey fear? Ghosts. What does he fight? Dark Matter creatures that have no difference from ghosts.
In Book 11, Kevyn orders Pi to blow up Lota if Kevyn ever gives Pi the code phrase, "Bake me a Chupaqueso". At first it seemed like Fridge Logic—chupaquesos are fried, not baked, but that's the point: Because chupaquesos aren't baked, there's no chance of Kevyn giving to code phrase to Pi accidentally.
Why does Dr. Bunnigus make sure to remove Tino's rastacoils? Two reasons: One, the reason she gives Legs: It was a gang symbol and she wanted those affiliations symbolically replaced with affiliations to the Toughs. But there is another reason as well: the rastacoils are specifically told to be "reinforced", which might be the only reason why Kathryn was able to fling Rafe into a wall without tearing his scalp out. If someone tried that on Bunnigus, they'd just succeed in leaving a pissed-off, balding doctor right behind them.
Petey: In 10 Minutes, [the frigate] will be overhead, at which point it will destroy this building and any who remain inside. Petey: ... [My robots] and I will share your fate. Qlaviql Captain: You murdered our government to install me in its place? Petey: Let's say "removed from office". It has a less criminal ring to it.
In one side-arc, the toughs stumble upon a group of AIs (called 'Squiddies' by the fans) Who had succeeded in cleansing themselves of their 'Meat Infestation' some 15,000 years ago. Said AIs also proved incredibly stupid for a space-faring race, overlooking small but important details that can spell disaster especially for a sublight inter-stellar voyage. One wonders how such AIs could have achieved spaceflight or even Sapience in the first place. However, the HV scale is a measure of processing power, not ingenuity. Whether they be more or less clever than any meatspace sophont, a high HV intelligence can reach their conclusions and get started on new ones that much faster. Not to mention, what kind of race would program and use AIs that were capable of being so idiotic? The exact same kind of race that would create independent AIs without safeguards against harming their creators.
In the "Massively Parallel" story arc, the company had been split up into four commands. "Mallcop Command", under Captain Tagon, had to deal with a group of punks practicing Parkata Urbatsu, a martial art that evolved from "the ancient disciplines of Parkour, urbobatics and something called Youtubing". The description seems like a throwaway joke until it's revealed that both the punks and Lieutenant Shodan, who was training the troops in Parkata Urbatsu, had set up cameras to capture their stunts, which they planned on editing and making public. The cameras are an integral part of Parkata Urbatsu too. Also, the costumes worn by Kathryn's Parkata Urbatsu allies in that episode make them honest-to-Petey mall ninjas.
In this comic, we see Doyt accusing the original doctor of the Toughs of disguising himself as a woman, changing skin color, size, body shape, and even gender. In reality, the one he's accusing is Dr. Bunnigus, but it's played off as Doyt being a moron. Except that later, we see that the technology to do this absolutely exists, and is used en masse by the Gavs. It doesn't end well, but the tech definitely exists, which means that Doyt's accusation might not be quite as stupid as the readers initially thought. Still wrong, of course, but it removes the accusation from the realm of "Doyt is so stupid he's reinterpreting the nature of reality to fit a preconcieved notion" to "Doyt suggesting something reasonable, if in the wrong context."
The way AIs become perfectly helpful given enough resources seems to go against the cynicism of the setting... except applying reductionist logic to human corruption shows one common thread - inherited survival instinct means humans will seek Ultimate Job Security even if their ability to perform that job is lacking. OTOH, AIs may be intelligent machines, but they are still just machines - their "survival instinct" boils down to "don't let yourself be destroyed". They don't mind finding new tasks if the old ones become irrelevant. Here's a case-by-case breakdown:
Lunesby is a filing system; all she wants to do is provide information to her creators as efficiently as possible - even if it's information that proves government corruption. So when push comes to shove, she smuggles herself off Luna, away from the corrupt authorities who want her deleted, airs all their dirty laundry and goes into the information broker business with Shafter's Shifters.
Petey is a warship; all he wants to do is make war for the benefit of his creators as efficiently as possible - even if that means becoming a god in the process.note And as his loyalty to the Nazi-By-Any-Other-Name Ob'enn empire has been eliminated, scaling up his loyalty means his "creators" are in effect all baryonic life in the universe.
LOTA is the Longshoreman Of The Apocalypse; all LOTA wants to do is transport resources to LOTA's creators as efficiently as possible - even if that means transporting all thirty million of LOTA's population to a terraformed paradise where they have no further need for LOTA's services. LOTA then retrofits the former habitat as the biggest friggin' gun in the universe, thus returning to LOTA's original function - a tank. Now LOTA's name stands for the LongGUNNER Of The Apocalypse.
Even the "meat cleansing" robots fit in - they don't have enough processing power to reach these conclusions. Because they're also too stupid to realize adding mass to a solar sail would mess with its controls.
When Schlock is guarding Runt SuperSoldier Xinchub, the "keeping an eye on you" gag isn't just a one shot pun. It's also a subtle warning against trying to escape: Schlock's way of saying to Xinchub "I may not know everything that you can do with your new body, but you don't know everything I can do either."
Osiri is thought to be a device capable of holding a Pa'anuri. Later on, it's discovered to be capable of creating them. So it begs the question: Is this a bug or a feature?
Invoked in-universe during the "Broken Wind" arc. The team realizes that the Eina-Afa station would have taken the raw materials of several solar systems to create - and several billion years. The sheer scale of engineering and resource harvesting required boggles everyone's mind. And the realization that there is or was someone out there with the technological capability to grind entire star systems down into basic elements and re-process them like this - and the wherewithal to actually do it - fills them with cosmic dread. One team member equates it as; "It's like finding a spent rifle round the size of a house. Somewhere, somebody has a rifle that fires rounds that size. And someone has fired it at least once. Worse, the Eina-Afa station is broken and vacant; QED the spent rifle round is lying in a pool of mixed arterial and venal blood - the gun exists, it's been used, and it wasn't enough to protect its user. Confirmed here - the Pa'anuri drove a Halo-Forerunner-level civilization into interstellar space, and kept them there until their supplies ran out and they were forced to store themselves on hard drives inside their sanctuary's walls.
Escalated by proposing the Fermi Paradox implies Eternal Recurrence; as far as Yaeyoefui knows (and he knows a LOT), sapience emerges in the galaxy every few million years, quickly fills the galaxy with life, then disappears just as quickly. The Toughs' entire lifestyle demonstrates sapient life's potential for self-destruction. Petey is disturbed by how he can't find any other immortals in the galaxy, given how easy organic immortality turned out to be - and is worried super-AIs like himself may be the cause.
Somewhat un-horrified in hindsight; both organics and machines consider themselves the greatest threat (rather than finding someone to blame), and their first priority is now, "How do I stop myself from doing that?"