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Season 1:

    Episode 1: Aftermath 
  • How is Crosshair missing almost all the shots in this episode? It makes his Improbable Aiming Skills look like an Informed Ability.
    • It has been demonstrated that clones can resist Order 66 and the inhibitor chip in general to a very limited degree, as shown when Rex warned Ahsoka about the imminent betrayal of her men right before opening fire on her. Presumably, Crosshair missing his shots at Caleb/Kanan and his former teammates during their respective fights is the true Crosshair persona resisting the chip-induced Crosshair persona.
    • Two things: one, everyone Crosshair shoots at in this episode have Plot Armor. If a young Caleb Dume was taken out or if Crosshair had managed to kill or capture his former teammates, then Star Wars Rebels would have never happened, and this show would be a lot shorter. Two, we’ve only seen Crosshair demonstrate his supreme marksmanship on Battle Droids up to this point, who generally lack any self preservation instincts. Snipers also prefer targets of opportunity, namely those unaware of the sniper’s presence. On both counts, the target was very much aware of Crosshair. It should also be noted that he did non-fatally shoot Wrecker so he could take out the others when they popped out of cover to help him, demonstrating that even with the chip, he still knows what he’s doing.
    • In Universe it is likely a mix of the above, as any Gamer who plays sniper in single player and then moves to multi player, firing on AI is a lot easier than people, who can adjust to a changing plan far more easily, and it is also possible that Crosshair is Fighting from the Inside, causing him to miss targets the real Crosshair wouldn't want to hit. Alternatively, if we assume that Crosshair's Improbable Aiming Skills are the result of a mental mutation we can speculate that Order 66 suppressing his true self may also be accidentally inhibiting his skills.

    Episode 2: Cut and Run 
  • How did Hunter know Cut on a personal level? Seems a little contrived...
    • Simple, Rex told him sometime after The Bad Batch arc in Season Seven, and sometime prior to the Clone Wars coming to their end, he and the Bad Batch paid them a visit and bonded. As for why Echo doesn't know is another thing entirely, since he would've joined the Bad Batch by the time that it became possible for Rex to tell them (seeing as the only other ones who knew were Jesse, Kix and Hardcase, and the former two hadn't met the Bad Batch prior to Anaxes and Hardcase died three seasons earlier).
    • Jesse, Hardcase, and Kix never knew about Cut. Sure they took Rex to the Lawquane farmstead after he’d been shot, but then they all took off to continue searching for General Grievous. They only ever interacted with Suu, as Cut only revealed himself to Rex later that night, and when Rex left, he was riding one of their farm animals to meet back up with his men.
    • You mean it's strange for a group of clones that have a penchant for not following orders to have a healthy relationship with a clone deserter who would be turned in dragged back to the army by most normal, duty bound clones? Hell, it wouldn’t surprise me in the slightest of Clone Force 99 helped Cut get away from the GAR, just as they help him get away from the Empire.
    • The Lawquanes lived on Saleucami, site of one of the Outer Rim Sieges - exactly the place the Bad Batch would have been sent for a mission, this being how they'd have met. As for why Echo didn't know, either the Kaminoans had got him on Kamino to recover from his prisony and test his augmentations during that particular mission or the Bad Batch was sent to Saleucami before Anaxes and didn't realize that the Rex they heard about from Cut was the same they met on Anaxes until later (something that would be perfectly in character for them, given how they forgot who they answer to) or simply didn't mention until they were alone with Rex due not knowing how the Regs would take finding out they found a deserter and didn't turn him in.
  • The kids look a lot more Twi'lek than in "The Deserter," in which they looked like a more even mix between Twi'lek and human. This is probably to bring them in line with Jacen Syndulla's look for Twi'lek-human hybrids, but is there any possible in-universe explanation?
    • Well, they’d be about four years older now than they were the last time we saw them. Honestly, I’d just chalk it up to Art Evolution.
  • Why did Tech not make Chain Codes for the Bad Batch while he was making ones for Cut and his family? Surely it'd be useful for them to have ones in case they need them.
    • The Batch are wanting to live completely off the grid. Even faked credentials can be tracked. Cut and his family aren't being actively hunted, and are not known to exist, so they can get by with faked ones.

    Episode 3: Replacements 
  • Why did that one Elite Trooper think it was a good idea to badmouth Crosshair (and clones in general), his commanding officer, in his face in the shuttle ride? And then afterwards attempt to usurp his command...by simply ordering his squad-mates to ignore Crosshair's existence during the execution scene? All the while, it didn't seem like that trooper expected any form of retaliation from him. In other words, why did that Trooper feel like he could get away with openly demeaning and defying Crosshair? Sure, that Elite Trooper's conscience wouldn't allow him to do what Crosshair ordered, but that still seems like a Too Dumb to Live moment on his part.
    • One possible explanation is the anti-clone sentiment detailed here on Wookieepedia. That would exacerbate ES-01's already arrogant character. Almost all of his lines reflect his belief that he's better than a clone. This shows up even in little things like refusing to get medically screened. Hopefully this sentiment - what the civilians thought of the Clone Wars - will be explored in future Star Wars media.
    • Also remember that he grew up in the Republic. The Republic had a lot of problems, but it sure as hell wasn't the kind of place where your commanding officer could execute you for refusing to follow an illegal order. He assumed he would be safe, because obviously the Empire is about punishing everyone else, right? It's a very common problem fascist supporters face when they actually get their fascist government.
  • Why would Tarkin send a probe to monitor the Bad Batch and ascertain how loyal they are, but not do so for the Elite Squad (who are arguably more of a wildcard than the Bad Batch - the latter were loyal to the Republic and were very efficient, but the Elite Squad are recruits that the Empire hasn't worked with before)? You would almost think that Tarkin and Rampart would actually want to see the performance of the Elite Squad, and whether they actually do as they're told, never mind evaluate whether or not they're competent replacements for the clone troopers.

    Episode 5: Rampage 
  • Why aren't the Bad Batchers shedding their armour already? They're known fugitives and the armour makes them stand out so much...
    • They need the protection and don't have the credits to buy other armor, especially of the same quality. Their fugitive status also doesn't seem to be widespread knowledge just yet, with Fennec Shand working on a direct commission hunt rather than a general bounty. Until news spreads more, they're just mercs in military look alike armor, a not uncommon sight in the galaxy. Changing their paint job would make sense, but merchandising man.
    • On a meta-level, there's no point to changing the signature appearances of the Bad Batch when their existing models work well enough, though if a second season is in the works it's entirely possible the Bad Batch will undergo Costume Evolution. In-universe, one can assume that as the Bad Batch are very protective of their identities, they don't want to get rid of their heavily-customized equipment as that gear is part of what makes them who they are. That, and as the Republic-turned-Empire is out for their heads anyways, they might as well use the high-quality military equipment said Republic-turned-Empire gave them, seeing as they have neither the resources or connections to come up with anything better.
    • In Rebels Rex and his crew of retired Clone commanders still had parts of there Kameno Armor works Phase II clone armor on them well in to the Imperial era with Rex even lampshading the trope of the poor aim of the stormtroopers as being because there helmet has low visibility compared to the clone trooper phase II that preceded it. In the Bad Batches case they recently escaped have no credits and they do take the armor off and go civilian when they need stealth. For them there biggest issue hiding is there custom Republic military shuttle they use for travel. The Early Empire is using the standard one as the executive shuttle until the Lambda class comes out.
    • At this point the galaxy is littered with the bodies of dead clones, it is more amazing that there have not been a lot of people seen wearing scavenged clone armour. Their armour really ought to not stand out at all. Unusual, but still relatively unremarkable.

    Episode 6: Decommissioned 
  • Would it have been possible for Hunter/Tech to have copied the tactical droid data onto another data stick, before giving the original to the Martez sisters?
    • It's likely that the tactical and strategic data it had stored was considered sensitive information. It's not unreasonable that they might have measures installed that make it more difficult to copy, than to merely transfer.
    • Remember also how in A New Hope, and to a lesser extent Rogue One, the Death Star plans were treated more as a physical object and less as data that could be transmitted, downloaded, uploaded, and copied. Maybe data protection is on a whole other level in the Galaxy Far, Far Away, where certain kinds of data can be wholly unique. Or perhaps they only had one data stick because they only anticipated needing one data stick.

    Episode 7: Battle Scars 
  • Does Echo know what happened to Fives? Rex hesitates twice when talking about the incident, the first time after saying the trooper’s name and the second after he tells Echo that Fives tried to warn him about the chips. Echo is probably aware that Fives is dead, but it almost seemed like Rex was choosing his words carefully so he wouldn’t give away just how he died. Granted, it probably doesn’t matter now because they’re all fighting clones, but maybe Rex is trying to spare Echo finding out that Fives was gunned down like a rabid animal by his fellow clones after being framed for attempting to assassinate the Chancellor.
    • It seems like that he would have found out at some point, given his lack of reaction to it. It's possible he was told, but the trauma he endured made it to where he wasn't able to process it properly. After all, he spent a year being tortured and used as a weapon against his brothers, and he's clearly a lot more numb and less personable than he used to be, so even if he was told point blank, he's too damaged on the inside to be able to react to it than if he wasn't.
  • Fives had to lose all his hair to get the chip removed in Season 6. Wrecker doesn't have hair. So why didn't Hunter and Tech lose their hair along with the chip?
    • Fives didn't really know all that much about the chip before he got it out, thanks to Rex's data the Batch knew exactly where to cut, presumably the medical equipment was precise enough to get them out without cutting their hair, Or the chip was not in fact covered by hair.

    Episode 9: Bounty Lost 
  • If Cad Bane is still able to gun down Hunter for the moment but then why is he having trouble with Fennec Shand?
    • Bane only had one quick draw to do with Hunter, who wasn't used to that. However, Fennec would have more experience fighting fellow bounty hunters, and she managed to close the distance to engage in hand-to-hand combat where she'd be better. Plus, Bane has had The Worf Effect applied, implied by the metal plate in his head hinting at the last duel he'd had (and lost).
    • There's also the possibility that Shand is just that good. She herself becomes a much feared bounty hunter (and later bounty herself) later on, and the legend has to start somewhere.
  • Retrospective headscratcher regarding the motives of Fennec Shand and her employer (now revealed to be Nala Se) in the fourth episode: if Nala Se was content to have Omega remain with the Bad Batch to keep her safe from Lama Su in the ninth episode, why did Shand attempt to retrieve Omega and keep her away from the Bad Batch back on Pantora? Did the objectives of Fennec Shand and Nala Se change in the interceding time (possibly due to the latter attempting but failing to reason with Lama Su about keeping Omega alive), and if so, why did Nala Se let Omega leave with the Bad Batch in the first place?
    • Nala Se only decided that leaving Omega with the Bad Batch was fine when Lama Su decided to cut losses and have her killed. Nala Se would still prefer her safe on Kamino, she's just willing to accept "safe not on Kamino" when the first option proves unlikely.

    Episode 11: Devil's Deal 
  • Is... Is Howzer's chip just not on? He has painted armor, a unique haircut, and the friendly demeanor of an un-activated clone. He seems to have been stationed under Cham for the war's duration. Who is not a Jedi, so maybe Order 66 did not apply to him? (One can only hope this means that one day he can escape the Empire's grasp)
    • You may have answered your own question (though I'm curious what the actual answer is, too). The chip might've not been activated due to lack of Jedi, and (based on his armor) being an ARC Trooper, Howzer might be a bit more individualistic than most clones and so kept the old colors.
    • Howzer has some pretty nasty scarring on the side of his face, and we know head injuries can interfere with the operation of the chip. It is possible that whatever gave him that scar reduced the chip's level of control over him.
    • We find out in Season 2 that the chip's imperative wears off after the initial order is given. It is possible that after the order was given that Howzer was as clinical as any other clone, but in the time since, coupled with the lack of Jedi around, the force of it has worn off and his personality has started to reassert itself.

    Episode 14: War Mantle 
  • Why does the Empire keep its prisoners in their armour? The series has models for the undersuits, so it's not likely to be a cost-saving measure to have Gregor and Hunter both in their gear while in a cell. They left Hunter with basically everything he had on him it looks like, which seems a rather bad plan unless they're wanting him to escape and lead them to the rest of the Batch.
    • In Gregor's case, its probably literal Plot Armor, allowing Scorch to actually come off as competent for longtime Republic Commando fans, while at the same time not actually killing anybody. In Hunter's case, its probably exactly for the purpose of allowing him to escape so he can lead Crosshair back to the rest of the squad. That actually seems like something Crosshair would do.
  • Why are the commandos shown using basic DC-15 blaster carbines instead of their trademark DC-17m interchangeable rifles? Gregor was previously shown to use one in The Clone Wars, and Wrecker is shown using this signature weapon in this episode. Even the argument that the average stormtrooper being trained at the facility won’t have access to that kind of hardware doesn’t really hold up because the other attachments for the DC-17m probably would have come in handy for stopping the jailbreak.
    • Just because it would have been handy doesn't mean they would have it. It's a training facility first and foremost, with a prison for special occasions. The commandos were wielding the weapons they were training the stormtroopers to use to do a better job, with their DC-17s in the armory for if they ever got shipped out. Considering they're being replaced and some clones have gone rogue already, it also makes sense to keep the best hardware out of their hands, just in case. The job is off the cuff and done without scouting so, despite it causing problems from lack of intelligence, the Empire also has no warning they're coming.

    Episode 16: Kamino Lost 
  • Why would the Empire send scouts back to a planet on which they just destroyed it’s only major population center? Tech seems pretty certain that they would and Crosshair stays behind to wait for them, but why would they come in the first place? To make sure the Bad Batch somehow didn’t escape? They didn’t know about the landing pad, so the Empire probably would have thought the clones would have nowhere to go if they survived the initial bombardment, and if they were expecting survivors why leave as soon as the city sunk?
    • In the Legends continuity the city that the Empire destroyed was very much not their only major source of habitation. Even in Disney canon, the tunnel system shown in this and the previous episode practically demands other cities or else the tunnels are completely pointless. Is the situation a bit questionable? Yes; at the very least Crosshair should've asked to be dumped on some other planet with a functioning spaceport. But it also makes sense to investigate the bombardment's aftermath, if for no other reason than to remind the remaining settlements that the Empire is still out there and in control.
    • It is always good military practice to assess the damage you've done after the dust has settled. Scouts would return to assess level of damage, and check for any survivors; hostile or friendly.
    • Yeah, the last thing you'd want after your intended display of terror and intimidation is for a week later a news crew to find 90% of the population alive on a floating but very damaged city, wondering what all the fireworks were about.

Season 2:

    Episode 1: Spoils of War 
  • Omega asks who Count Dooku is. Since he is the de facto leader of the enemy her clone brothers were made and trained to fight, shouldn't she know this already?
    • Dooku, as Tyrannus, also hired Jango Fett to be the clone template. The fact Omega has been in Nala Se's lab for most of her life, and is a literal child, she probably never much cared for the politics of the Clone Wars.
    Episode 8: Truth and Consequences 
  • After the atrocity Rampart committed on Kamino is made public, Palpatine appears, and condemns first Rampart, then the clones, claiming that they were blindly loyal and carried out Rampart's orders without hesitation, and he used that as ammunition to discredit them. Was that not what he wanted this whole time though - a fanatically loyal army that would obey their orders (even ones as extreme as bombing their place of creation to the bottom of the ocean?) no matter what? Why would he use the very thing he sought in the Imperial military (loyalty to the regime, which he did get with the stormtroopers that succeeded the clones) to paint the clones in a negative light?
    • Palpatine only wanted the clones for one purpose — kill all the Jedi. They've served that purpose. And in his arrogance, he decided they no longer had any place in his new Empire. Luke did say that his overconfidence is his weakness, and Palpatine thought that with the Jedi gone (or at least wiped out enough to where it would be extremely difficult, if not impossible, to recover fully), he didn't need a army of trained Jedi killers to enforce his regime when an army of conscripts could be cobbled together much quicker and at a far greater number than any clones could, especially since said clones would die within a few years given their accelerated aging. The Empire could just recruit more men to replace the dying clones from any number of systems, conquer another world, then recruit more, rinse, repeat.
    • He used the "dogmatic loyalty" excuse but the issue was that the clones were increasingly showing signs of independence and second guessing their nominal employers. Not all of them to the extent of the Batch or Rex's operation but enough that a clone uprising could be dangerous and difficult to put down.
    Episode 11: Metamorphosis 
  • Yes it's the empire and it's evil, but why exactly do the Imperials abduct all the citizens just for seeing the Zillo Beast clone? It's not like anyone on the planet would discover Emperor Palpatine's secret cloning facility and a mass abduction would raise more questions than if they just annexed it under the pretense of helping them rebuild their cities.
    • The villagers saw a creature that was believed to be extinct by many people, and within just a few minutes of it chowing down on energy from their power plant and growing huge, the Empire conveniently shows up and captures it. You can put two and two together and assume that they have something to do with it - not only the fact that an extinct apex predator was brought back to life, but that the Empire showed up and captured it rather than killing it. As a result of being in the wrong place at the wrong time, the villagers are witnesses, and witnesses have a habit of telling others what they witnessed. That's something the Empire couldn't afford to have happen. A mass abduction of a small settlement on some backwater world, on the other hand, is way easier to cover up than the Empire's involvement in the return of the Zillo Beast species, and if you abduct all of the witnesses and no one witnesses that, you're safe. Plus, as we saw a few episodes earlier in the midseason two-parter, the Empire covered up Rampart's actions on Kamino as a natural disaster, and the galaxy bought it until footage of the atrocity was shown to the Senate, so no reason to assume they couldn't pull something similar if they really wanted to.
    Episode 14: Tipping Point 
  • I might've missed something in the previous episodes, but it certainly wasn't established in this one - how did we go from the Empire believing the Bad Batch was KIA on Kamino, to Dr. Hemlock asking Crosshair about them as if we're back in Season 1, where the Empire knew the Bad Batch had escaped. Only three major characters in this season - Crosshair, Rampart, and Wilco in the season premiere - knew, except Crosshair and Rampart, as far as I know, never told anybody, and Wilco was going to put it in his report before he was killed by Rampart. That just leaves Crosshair and Rampart, who both knew that the Bad Batch survived, but they never mentioned it to anyone (something like that would've/should've been shown on screen) and yet the Empire somehow knows that the Batch is still alive. How?
    • The Batch have continued operating throughout the season, making it possible for the ISB to learn they are still alive. Additionally Nala Se did inform him about Omega, and we know Cid flipped on the Batch at some point. Additionally it's possible Hemlock just figured out he was lying in the first place.

Season 3:

    Episode 14: Flash Strike 
  • Did the Bad Batch really have to follow the ship all the way to Weyland? Considering how careful they were trying to be in expecting security headaches since the previous episode, you'd think it would occur to them to let Echo go ahead of them and track him through his comm link, which he clearly used when he got on board the ship. If not that, they could've at least just detached immediately after exiting hyperspace and watch the science vessel enter Weyland from a distance to make sure Echo gets there. At least with either of these methods, they could've avoided most of the problems that happened in this episode even if news of their stunt got to Hemlock. Plus, Echo could still transmit them and Rex the coordinates.
    • If Echo sends a transmission from the enemy ship, it would be detected, and thus the Empire would know that not only is there an enemy agent aboard their ship, but said enemy agent is transmitting their coordinates to his allies. Couple that with how the Empire realized that the Batch had infiltrated their station over Coruscant, and the end result is that you're looking at Tantiss being on high alert and way more heavily fortified.
    • Well yes, they could do that, but that just brings even more risks. The group probably figured that it would be a lot safer if they went it themselves, especially since this looked like a suicide mission which could still go wrong in a million different ways already. Plus, if Hemlock so much as suspected that the Bad Batch was on their way to Tantiss, he likely would have tightened the security even more than it already was, making our heroes' odd even worse than they were already.
    Episode 15: The Cavalry Has Arrived 
  • If the Zillo Beast's armor is impervious to blasters, explosives, etc., basically anything that isn't the gas they killed the original one with in The Clone Wars or the stun beams that were used in TCW and this show, then why would Dr. Hemlock essentially just throw away two entire divisions of TK troopers that could've helped stop the Bad Batch's incursion? The Empire could always track down the Zillo Beast (which, I might add, was fleeing, not sticking around and causing havoc during the Batch's incursion) later. All that - and calling off air support - did was make it even easier for the Batch to carry out their mission.

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