In Airship, when facing against the Right Hand Man, regardless of what battle style you choose (Final Fantasy or Earthbound), Henry wins if you choose the items/goods option. This is appropriate, since throughout his escapades, Henry's only been good at using items and gadgets. This even remains consistent with the Undertale-style battle with Mr. MacBeth that appears in Mission. This is also why Henry seemingly Took a Level in Badass in the Executive/Betrayed route in Mission. With cybernetic enhancements, his whole body is a gadget.
In Complex, Markiplier and Jacksepticeye make cameos as prisoners. This makes sense when you remember that they've played the games before, and thus, they've helped Henry pull off his crimes!
Obtaining the "Presumed Dead" ending in Complex requires you to let the decision timer run out, something that has always meant certain death up until this point. The "presumed" part could refer to the player just as easily as the complex staff.
In the "Presumed Dead" ending in Complex, When Dmitri says that this is coming out of the guards' paychecks, he's not just referring to Henry's escape. He's also referring to the van destroyed in the incident.
Why does Reginald grow to accept Henry's leadership of the Toppat Clan in Mission's Executive/Allies and Executive/Dead routes? Because in Airship, Henry only assumed leadership by usurping Reginald, a gamble that Reginald had to make or else the entire clan would have been crippled by the government. In the process, Henry betrays his initial employers to satisfy his own Greed. Someone like that is hardly the person you want commanding a team of people (criminal organization or otherwise), leading Reginald to happily betray Henry in Complex's Betrayed route. However, in Mission's "Toppat King" and "Toppat 4 Life" routes, Henry puts himself at risk to protect the clan, proving he has their interests at heart rather than his own and finally earning Reginald's respect and trust.
Reginald became the Toppat's then-current leader to begin with because he was the one who killed the previous leader Terrence Suave, a Pointy-Haired Boss who kept blowing resources on nonsensical raids for fun. Thus, he's so eager to betray Henry in "The Betrayed" and "Toppat Civil War" not just because of his own virtues, but also because he can't possibly stand to have someone like Terrence rule again right after him. It also explains why, in the Executive/Ghost path, Reginald is so willing to capitalize on the opening to overthrow Henry that Ellie provides. Henry still hasn't earned Reginald's respect in that path, so Reginald was still planing to betray Henry.
Why did the other Toppats initially accept Henry as a leader? Alternate Character Interpretation. For them, Henry is a fellow criminal who was captured by the Government and forced to work for them; but as soon as he got the chance, he managed to free himself, screwing the Government over. On top of that, Henry defeated both the Right Hand Man and Reginald - and therefore, by the Clan's standards, he has the right to be their leader.
In the Executive/Betrayed path of Mission, Henry is revealed to possess a Spirit (named "Reference") whose ability is to access different timelines. This is not just a shallow reference to D4C, as it contains several pieces of brilliance:
If you think about it, every path (sans Bank) and ending in the whole series can be considered as alternate timelines, even the failures themselves. Thus, it's only natural for Reference to be able to hop between timelines and guide Henry to victory, just like how the players do.
Reference's battle cry, "failure", references just how Henry has failed over and over across different routes.
If Henry's medical report in the Lawyered Up route of Prison is to be believed, then it means that Henry did try every option in Bank before landing on the disguise option. Considering the other options end up in a massive failure that injures him, it shows that no matter what, Henry will always try every option available to get what he wants. Having the ability to access different timelines is a natural fit for someone like him.
At one point in the battle, Henry and Reference swap places with each other. This could be explained as him simply accessing a timeline where he and his spirit are in a different position, and then applying that to his own timeline.
If we assume that Reference's core ability is to send the target in an alternate timeline and force them take the role of the alternate counterpart (hence why the Right Hand Man lost his cybernetic augmentations when he was punched into the other timeline), there's another explanation. A Stand is a part of its user, and it can be interpreted as an alternate version of them; therefore, Reference can take Henry into another timeline and have each of them take the other's role - the Stand becomes the user and vice-versa. So, if Henry and Reference travel into the same timeline they started from, the end result is that they switch places.
If the "Ghost Inmate" path is chosen in Mission, "Toppat Civil Warfare" is the only combination route where Ellie seeks revenge on Henry for abandoning her. Why only that specific one? In the "Pardoned Pals" path, she reveals that she is familiar with the Toppat Clan and knows how to find them, which is why she can chase down Henry if he leads the Clan. "Cleaned `Em Out" and "Jewel Baron" contain no connection to the clan, and "Free Man" has Henry captured as a personal vendetta by the Right Hand Man without involving the other members of the clan. Thus, a casual acquaintance like Ellie would not be able to find him.
Another thing to consider is Henry's notoriety. Of all the four ranks in Airship, Henry is only the most notorious as the leader of the Toppat Clan. Government-supported private investigators, master thieves, and master bounty hunters are plenty out there in the world, but there is only one Toppat leader at a time.
Why is Henry only chased by the Wall in the Thief/Allies route? Because in the Thief ending, Henry became the enemy of both his government and the Toppat Clan, making him especially notorious. Plus, Allies is the ending of Complex that tarnishes the name of the Wall the most, with a full-scale prison riot. Only with these two powerful incentives do the forces of the Wall chase Henry and Ellie all the way to a tropical jungle.
It's also possible that the Wall was able to track them in the Thief/Allies route simply because they were still riding the motorbike they used to initially escape. Given that it was part of the Wall's fleet of vehicles, there was almost certainly a tracker embedded in it, which they used to follow Henry and Ellie to the launch site. Every other path clearly has them ditching the bike at some point, either by swapping out for Henry's tank in the Bounty Hunter route, hitching a ride with Charles in the Investigator route or finding a way to rejoin the Toppats in the Executive route.
One background detail during the Undertale fight in Mission (Bounty/Dead path) is that Henry is LV 18. Anyone who's played Undertale to the end should know the significance of this detail: Henry's Level of Violence has been raised above the minimum because he's taken lives before, which is exactly the case considering how many prison guards and Toppats Henry has killed in pursuit of his varying goals over the series.
The reviews on the devices made by Gadget Gabe could be past reviews referencing the year the original games were made. This could be how the events of the series take place only over a year.
The CorrupTick messes up the software and corrupts the code. It is a literal bug.
In some of the routes of Mission, the Right Hand Man has been turned into a cyborg after Henry defeated him in Airship; his legs, right arm, and head received cybernetic implants or were replaced entirely. In the Executive/Betrayed route, Henry is also turned into a cyborg, with augmentations to the remaining parts (spine and left arm).
During the choice where you have to decide between three same hammers in the Thief/Dead route, the positioning of the choices actually hint at how the hammer will be used. The left hammer has you use the hammer on the left side of the screen. Since there is nothing but the glass on the left side, Henry will whack at the ceiling unsuccessfully until he gets shot. The middle hammer has you use the hammer on the middle of the screen, which is where Henry is. He will use it on himself. The right hammer has you use the hammer on the right side of the screen. The sniper is firing from that side. So the logical turn of events would be Henry swinging the hammer to the right, hitting the bullet in mid-air back to the sniper. On top of that, there is a second hint. This is literally the right hammer.
All the teleporter failures (and successes) have always sent Henry to a tangible place, except in Airship where it simply sent him to an empty void, and it makes sense why. If you look closely, in all other teleporter scenes (barring Airship and Mission), he always presses the bottom button, top left button, and the middle red button, in that order, and only once per button. However, in Airship, he pressed the top left button twice instead of once. That may have caused the teleporter to malfunction.
Choosing to side with Charles in the Thief/Allies route has him recruit you and Ellie to take out the rocket's support beams with mounted machine guns. The Fridge Logic would be why they apparently couldn't spare a couple more soldiers to be in the helicopter to do that instead. The Brilliance comes in when you remember an earlier choice: when you and Ellie are pursued by a pair of soldiers, the correct choice is to go back in time and get those two ejected from boot camp, resulting in there being no-one to pursue you. The helicopter that they jump out of is the same kind that Charles is piloting, so they were probably the two assigned to do just that before Henry messed with the timeline, and since they were already pulling out all the stops for this (as mentioned in a couple other routes), they might have been stretched thin enough that there was no-one else they could assign to that role.
Doubles as a Fridge Tear Jerker. You wanna know why they opted to make Valiant Hero so depressing? ...The guy who got Charles killed is named Jacked Hughman. And if you're gonna name a character after the guy who played Logan, it's only a matter of time before your audience is drenched in tears.
When you do the International Rescue Operative ending in Complex, Charles mentions that he's on a mission, but should have enough time to pick Henry up. Mission often starts with the Government raiding the Toppat Orbital Station in hopes of destroying it, and the Bounty/Operative ending has Henry still on Charles' helicopter, moments before the raid begins. Charles was mentioning the battle with the Toppats all along.
During the TCW route, when Henry is forced to walk the plank, he can use a chainsaw to try and invoke cartoon physics, but it doesn't work. While this could be a case of Reality Ensues, it could also be because whenever the joke happened in cartoons, the person that falls is always the one cutting the wood. So, in short, Henry could've avoided falling by giving the chainsaw to Ellie, and the fail would be for a different reason.
On their own, Reference and Bottled Time seem like really generic Spirit names, but once one considers that they're a play on the subtitle censorship of the JoJo anime, they can look at their Stand names, and come to realize that their actual names are song references. Reference is actually Tribute, the name of a Tenacious D song, and Bottled Time is actually Time in a Bottle, the name of a Jim Croce song.
In the Government/Ghost route, Charles doesn't appear at all. Why? Every game had a sneaky ending (Sneaky Escapist, Unseen Burglar, Government Supported Private Investigator and Ghost Inmate), so to follow the tradition, Mission also needs to have one. However, considering what is Charles' definition of a great plan, he had to be cut from the route. Besides, Charles wouldn't side with Henry as in this route, Henry doesn't plan to bring down the Toppats, just steal something from them.
Why did Geoffrey and Thomas stay loyal to Henry in the Executive/Ghost route? Part is because Henry is legitimately a good leader, but part is also because they noticed how quickly Reginald pushed for a mutiny without giving Henry a chance to explain himself. And when the two tried to question Reginald's actions, the Right Hand Man immediately imprisons them in the brig. So they probably came to the conclusion that Henry is actually innocent and Reginald was just attempting a coup. Even if they were completely wrong and Ellie was right...
Why does Reginald care so much about Henry betraying Ellie (a girl he literally just met) despite the fact that Reginald is all to willing to betrayHenry in The Betrayed? It's simple: he doesn't. Reginald was always going to betray Henry, it was just that Ellie arriving and stating that Henry abandoned her gave him a good excuse to do just that in a way (most of) the Toppat Clan would back him on.
In Airship, Winston Davis (the guard that unknowingly smuggled Henry into the bank) can be seen in the Earpiece route, having become a Toppat member. If you choose the Disguise option, he's the one who treats "Smith" with the most suspicion - because he's the only Toppat who has already seen Henry before, and he lost his job because of Henry. No wonder he almost recognized him.
Reference is a combination of Hierophant Green's design, Dirty Deeds Done Dirt Cheap's alternate timeline power, and Gold Experience Requiem's speaking ability, and with those three aspects in mind, you'd think that Henry would have an easy victory against the Right Hand Man and Bottled Time. ...However, what's worth noting is that D4C and GER are seen as some of the most overpowered Stands, whereas Hierophant Green is often seen as worthless. And when you consider that RHM's Spirit is based on The World, anything resembling Hierophant Green doesn't stand a chance. Doubly brilliant when factoring in that Reference being a combination of two overpowered Stands and one very weak Stand directly mirrors Henry's incredibly inconsistent luck.
The people that Henry can meet in the Tavern (by picking one of the Dead routes in Mission) directly reflect the state of the Toppat Clan after the events of Airship. From strongest to weakest:
Executive/Dead: Henry has become the leader (and is implied to be better than Reginald), Right Hand Man has become a cyborg, and nobody was arrested. Both Icepick and Snowcap are present in the Tavern - but there's also a couple of soldiers that don't appear in any other route. Presumably, the Government called for extra soldiers precisely because the Toppat Clan is so strong in this route.
Bounty/Dead: The Clan has lost Reginald, but RHM has become a cyborg and succeeded him as the new leader. Both Icepick and Snowcap are present.
Government/Dead: Following Henry's mission, Reginald, RHM and many other Toppats were arrested, and the survivors are now led by the inexperienced Sven. Neither Icepick nor Snowcap appear, so we can assume that they were arrested as well.
In Airship, if you choose to steal the ruby, the Toppat Clan and the Government eventually face off in the desert. However, the Center for Chaos Containment tries to solve the situation by putting one of 4 discs into a machine. All but one kills Henry, and sometimes it destroys the world too. This would be less terrifying if the guard wasn't INSERTING DISCS AT RANDOM, which means that the people in charge of the deadliest weapons in the world don't know what they are or what they do. Also compounded by the fact that the Government didn't know what was there, implying that a random company has more advanced tech than the Government.
In the "Presumed Dead" route Henry can goes to a random building, only to be greeted by Freddy Fazbear who presumably kills Henry. In the Convict Allies route, Henry accidentally releases all the convicts causing a Prison Riot. There is a slight probability that some convicts entered Freddy's building and got killed by him.
The "Triple Threat" ending has the Toppat rocket sent to the Wall, thus dooming them to life in prison. Except er: the Wall just suffered a mass breakout which resulted in a massive amount of damage and casualties, and Henry just sent a station filled with experienced criminals into the dead center with access to their weaponry. Best case scenario has them still being arrested even with the damage done to the Wall. Worst case scenario has the Toppats take over and making the complex into their new base with a bunch of new recruits while the Warden works with the Toppat clan to go after Henry and his allies.
In the Thief/Allies path of Mission, both The Wall and Henry's Government don't recognize each other, even with The Wall knowing who the Toppat Clan is. The Wall refers to the latter as, "some other government," whereas Henry's Government doesn't even know about The Wall, referring to them as, "Toppat reinforcements". Even Reginald doesn't know about The Wall in The Betrayed path of "Complex" until Henry tells him, and the only ones who seem to be aware of The Wall's existence are Charles, saying that he thinks he's heard the name before, Smith, who works as a double agent for The Wall and the Toppat Clan, and Wallace Pemberton, who is an undercover agent allied with the Toppats. Makes The Wall come across as a very shady penitentiary, which only begs the question, how has The Wall gone undetected by different governments of not only the Earth, but also the entire universe (if Gus Garno being implied to have been a podracer is anything to be believed), for this long to apprehend notorious criminals?
In Thief/Ghost route of Mission, it's revealed that the Toppat Space Station has a Kill Sat called Supreme Dominance. Given that the idea of the space station is to simply have a secure base while being able to steal anything beyond the reach of Earth's governments, why do the Toppat Clan need such a ridiculous weapon in the first place? In the routes where they already have the station up in orbit, could they have possibly used the laser before Henry showed up? If so, on whom?
Fridge Tear Jerker: The only time Charles sounds even remotely panicked throughout the entire series is when he's telling Henry to leave on the escape pod in the Valiant Hero path, and he calms down once the pod takes off and Henry's out of danger. From this, we can infer that one of the few things that can rattle Charles is the idea of his close friend's life being in peril. The opening cutscene confirms that Charles did hear the supposed news of Henry's death (Presumed Dead is one of the necessary endings for this path). How did he take that news? Probably not much better than Henry took the realization that Charles died on that space station. What further drives this home is how ecstatic Charles sounds at seeing Henry again at the beginning of the path, giving off the impression that he really was hurt by Henry's faked death. The fact that Charles cares so much about Henry's presumed death even though they barely know each other (they literally worked together once in Airship) may imply that Henry was the closest thing to a friend Charles had.
The fact that Charles gave Henry the communicator in Cleaned 'em Out (there's a sticky note on it that says "from: Charles :)") implies that they did keep in touch to some degree after the events of Airship. (This is also a Government route.) So Charles definitely considered Henry more than just a temporary partner recruited out of desperation, and they likely maintained at least some sort of contact prior to the events of Complex and Mission.
In the Government/Rescue route, Charles mentions that there is no chance that he'll accidentally shoot Henry with the IR sniper rifle. This is of course a reference to the fail in Complex where he accidentally shoots Henry. However, since that didn't actually happen, just whom did Charles accidentally shoot to necessitate switching to the IR rifle?
In the Convict Allies ending, every cell in The Wall has been opened... but does that include the quarantine cell?