[[folder: Darkness Rising, Part 4 ]]
* Why does Bulkhead ask Miko to look away when he's fighting the Vehicon? From his perspective, he's ripping someone's heart out, which is certainly not suitable for kids, and he knows it.
[[folder: Darkness Rising, Part 5 ]]
* Ratchet not knowing about the large radio antenna array is a prelude to the episode where he's unable to help Raf. Just as he wouldn't have bothered to study human medicine, given that he doesn't think highly of human technology, he naturally wouldn't have looked at that either.
[[folder: Convoy ]]
* The "minimal force" used against M.E.C.H. seems excessive, as in [[EveryCarIsAPinto blown up cars]] excessive. However, that kind of force would have been minimal ''against Decepticons''. Clearly, human vehicles are more fragile than what the Autobots are used to fighting, making this a collective DoesNotKnowHisOwnStrength.
[[folder: Deus Ex Machina ]]
* Starscream's disdain for an automobile alternate mode makes more sense if you remember that a good portion of the Vehicons, the ''minions'', turn into cars. To Starscream, not only does it lack the perks, but also, to Decepticons, flight is a symbol of status and command.
** It could also be seen as faction divisionism, since the Autobots seem to prefer car-based alternate modes in general. It may explain why Knock Out is considered such a ButtMonkey even by his fellow Decepticons.
[[folder: Rock Bottom ]]
* Rock Bottom is often a term where a character hits at his/her lowest emotional and psychological state. When the mine collasped, the five characters( Megatron, Starscream, Jack, Miko, and Bulkhead) all hit into a desperate situation with little to no help coming soon and we see how they react to this situation, revealing [[WhatYouAreInTheDark what they are in dark]].
** For Starscream, although given the chance to [[TheStarscream abandon]] Megatron to his fate, we see that he would rather risk his own life to save Megatron for his master's respect than live his life as a Rogue while the other Decepticons get all the credit for Megatron's rescue.
*** Part of this was pragmatism on the account that, well [[NoOneCouldHaveSurvivedThat after surviving the space bridge explosion]] Starscream was smart enough to recognize Megatron's capacity to survive the impossible. It also serves as fun foreshadowing into future plots, since Starscream gets PutOnABus the very next episode in opposition to what happens in Rock bottom, and much of season 2 is spent with Starscream squaring his ambitions with his rationality and pragmatism over what he REALLY wants out of life.
** Megatron, on the other hand, doesn't fear death even when it's right at his face. He reveals himself as ideal and moral corrupter, [[HannibalLecture goading]] Jack to kill him right now at this helpless state because Optimus would. If Jack does kill him, then he has proven that the Autobot morals are easily corruptible and that [[HeWhoFightsMonsters they are no better than Decepticons]]. If Jack doesn't however, then Megatron lives and would continue to reek further atrocities, thereby ruining any chance of ending the [[WhyDontYouJustShootHim the war]] [[WhatTheHellHero quickly]]. Either way, Megatron [[XanatosGambit wins]].
** When Jack Darby is trapped and separated from his partner Arcee, he shows that he is capable of handling the situation with no one around, quickly finding a drill machine and using it to tunnel his way out and find the others. When Jack was given the chance to kill Megatron, he did not relinquish Optimus Prime's ideology even if it could end the war.
** When Miko and Bulkhead are trapped in a cave, with Bulkhead holding the ceiling and level of oxygen decreasing, both of them show a side of concern and care to the other. Miko, despite being unable to dig her way out or fight decepticons, is more than willing to try to save Bulkhead from being crushed under the ceiling and reluctantly leaves him behind for her own safety. Bulkhead's first priority is to get Miko out immediately before focusing on his problem. When Starscream threatens to attack Miko, Bulkhead demanded that Starscream deal with him alone despite his disadvantage.
** We don't see much of Arcee in this episode despite her being one of the causes for the cave-in, but the truth is She already hit her rock bottom. In fact, the bitterness of hitting the bottom was how Jack found her way back in Darkness Rising. She already experienced the despair of "no way out" under Arachnid, and so all she can do now is move to help the others out of their predicament since she's been there, done that.
[[folder: One Shall Rise, Part 1 ]]
* There are some goofs, like some grammatical errors and Optimus stating that Earth's core is full of lava as opposed to magma, but these are AliensSpeakingEnglish. It takes us long enough to learn the language of the country next door to us! And, even if these guys use the internet like their movie incarnations, who's to say that they didn't pick up some dodgy urban myths while doing so? Besides, none of the humans present seem like the types to care (or know) of these errors, and the 'Cons are the ones making most of them, especially Megatron; the guy who spent three years in space, thinks HumansAreBastards and refuses to sink low enough to take an "native" alt mode.
** Not to take away from the main point, but A) complaining about lava vs. magma is like complaining about using the wrong meteoroid/meteor/meteorite, and B) the core isn't made of magma, either; that's the mantle. The core is made of metal.
*** ''Living'' metal...making it a stealth double Fridge Brilliance looping back on itself!
* It seems that, for all his ChewingTheScenery, Unicron's power is finite, given that he can create a single Mook capable of talking and over powering Optimus, but an army speaks in unison and does about as well as Megatron's mooks. The giants he creates later seems to be incapable of anything other than dull movements, such as scraping the ground and walking slowly.
** [[spoiler: Of course, Unicron was never fully awake during the entire season 1 finale, as that would have destroyed the Earth. A fully-conscious Unicron could probably split his consciousness more ways than a semi-conscious one could.]]
* Given [[spoiler: Unicron is one with the planet Earth and energon is cybertronian blood, they're basically taking Unicron's blood. But more than that, ''humans'' might also be doing the same in the form of things like oil and geo-thermal energy...]]
** Which actually justifies [[spoiler: his condemning humans as "parasites." After all, how would YOU feel if you found out somebody's been stealing fluids and tissue from your body while you were asleep?]]
** Mind you, [[spoiler:the minerals we use generally ''aren't'' from Unicron - he is just the Core of the Earth, and things like oil and metallic ores found their own way here, so the argument isn't really as valid (we haven't really gone beyond the Crust, let alone hit the Mantle or the Core). Back to square one for the most part - he'll kill use just because our existence is an inconvenience to his waking up. Then again, he ''is'' MadeOfEvil... we shouldn't really expect much empathy from the Cybertronian version of TheDevil.]]
* When Unicron uses his first avatar to initially attack Optimus, Optimus instead pauses and attempts to reason with him first instead. Surprisingly, Unicron halts his attack and seems interested in hearing what he has to say. Why? Well, if one remembers that The Fallen was once a Prime who fell to Unicron's influence, then there's a good reason why Unicron would hear Optimus out; to see if Optimus himself would also be willing to make an offer of servitude.
[[folder: One Shall Rise, Part 2 ]]
* Some people complained that Megatron hearing Rachet's communication with Arcee in this episode was a continuity error. However, if you watch some of the earlier episodes you'll notice that Soundwave is somehow able to pick up transmissions between Autobots. Somehow, he might have been able to break the code, allowing them to hear Arcee's position, Wheeljack's arrival, and Optimus's troubles with MECH.
* Jack refusing to take the bait from Megatron. Jack made that mistake with the school bully back in "Speed Metal," and got in trouble with every Autobot, Decepticon, and human involved. Lesson learned!
[[folder: One Shall Rise, Part 3 ]]
* Earlier in the series, Starscream spends a lot of time trying to get around Soundwave rather than directly challenging him whilst in command of the Decepticons. Then this season finale comes along and Airachnid doesn't think she needs to. Cue Soundwave utterly [[CurbStompBattle owning]] her and forcing her to yield. Starscream was worried about getting his skidplate kicked if he tried anything too ambitious.
** Also note that, in the fight, Airachnid doesn't land a single damaging blow onto Soundwave. Why? Because Soundwave is a scout; it's his ''job'' to watch people and listen in on them, meaning he's been watching Airachnid's moves, and accordingly created a strategy.
*** It's possible that Soundwave was defeated by Optimus in "Minus One" because he has barely seen the new Optimus in action.
** Ratchet mentions that Soundwave's loyalty was important for Megatron when the latter was leading his revolution. This seems like a offhanded mention at first. However:
*** In "Masters And Students", Starscream refuses to investigate Megatron's detected life signal...a decision he quickly reconsiders out of fear of displeasing Soundwave.
*** In this episode, the Decepticons were all ready to rebel with Airachnid against Megatron until Soundwave thoroughly stomped her into the ground.
** The Decepticons are more loyal to ''Soundwave'' than Megatron. Why? He was the only Gladiator in Kaon that could have bested Megatron. No other Transformer, not even Optimus, holds this title.
* Why Bulkhead is the only one affected by Dark Energon: all the others have already come into contact with it; it's keeping Megatron alive, Optimus has fought a bunch of Terrorcons and was in the midst of a Dark Energon eruption, Bee directly handled a shard of it in episode 14 and was hit with the stuff in episode 23, and Arcee was infected with it way back in episode 2.
** This also helps to explain why Bee recovered from the dark energon effects of Megatron's blast fairly quickly even though he should've gotten sick from it like Raf did.
*** Well, yeah. Arcee and Optimus only had second-hand contact with Dark Energon that was probably diluted with other ssubstances (non-Energon fluids from the zombies, soot and ash from the volcano). Bee, however, spent a good portion of an episode with a concentrated amount of undiluted Dark Energon in his hand.
* The writers have found a way to kill Optimus without breaking their rule that when a characters dies, they stay dead. By having Optimus loses his memories as a Prime, and worse yet, join the Decepticons, in effect, Optimus Prime is dead.
* Megatron is briefly possessed by Unicron, and appears to be in flames. [[InternalHomage Consider the source of Megatron's name]]. If one is not savvy on the mythology of ''Transformers'': Megatronus Prime would later go on to be known as The Fallen.
* So why did Unicron have an eye inside his own body. 2 reasons: 1) [[DangerouslyGenreSavvy he finally caught on]] [[MythologyGag to the fact that]] [[TransformersTheMovie anyone who]] [[TransformersArmada wants to defeat him]] [[TransformersEnergon will enter his body to do it,]] (2) He realized you can't fly a ship through his eye when it's on the inside.
** There's also the fact that despite having transcended physical form, as Optimus states in the season finale, he also still has a physical form that he can and as shown by his spark being still within his spark chamber, ''does'' inhabit. As such, being a god, he can pretty much do anything he wants to his own body.
** He's in his alt mode, and the eye is part of the KibblesAndBits.
[[folder: Orion Pax, Part 1 ]]
* Agent Fowler asks, "Why send a boy to do a Bot's job?" To me, that was a good question - why ''would'' Optimus make Jack the only one who can [[spoiler: restore his memory]], when the other Autobots are more likely to survive to finish the job? And this is more than Optimus trusting in Jack's maturity; the other 'bots have been with him far, far longer than the humans have. But Optimus gave [[spoiler:the Key to Vector Sigma]] to Jack because he knows Megatron's disdain for humans in general: when Megs was waiting on the other side of the [[spoiler:Space Bridge]], he was expecting ''Arcee'' to [[spoiler:hold the Key.]] But when Arcee arrived, she fought him instead, buying Jack enough time to [[spoiler:restore Optimus's memory.]] Optimus knew what would happen when he [[spoiler:unleashed the Matrix on Unicron]], anticipated what his team would try to do - and found the one factor he knew Megatron would overlook.
* [[spoiler: Starscream returning to steal energon makes perfect sense when you think of the fact that all transformers use energon to function. Starscream doesn't know where the autobot base is, so it makes sense that he would come back aboard the decepticon ship to steal cubes for himself.]]
[[folder: Orion Pax, Part 3 ]]
* So Optimus' Matrix of Leadership was reformatted, and Jack had to retrieve a new copy of the data. Jack was in possession of the only active copy of the Matrix. Jack was, temporarily, a Prime.
[[folder: Operation: Bumblebee, Part 1 ]]
* Bulkhead seems quite panicky at the thought of Optimus finding out that he's taken Bumblebee out on a scouting mission with him. This may be because he got told off for doing the same thing in "Darkness Rising" with Miko!
* Now that we know Bumblebee was tortured and maimed by Megatron himself, his actions in Sick Mind/Out of His Head take bravery to a whole new level.
[[folder: Loose Cannons ]]
* In this episode, Wheeljack is initially distrusting and not entirely respectful of Optimus Prime, viewing him as the kind of commander who would rather put his troops in danger than himself. Now, in this universe, Wheeljack and Optimus have never directly met or worked with one another before, so it makes a little sense that Wheeljack might judge his character wrongly. It makes a ''whole lot'' more sense, when you remember [[http://tfwiki.net/wiki/Sentinel_Zeta_Prime who the previous leader of the Autobots was]] in this universe and that his [[BadBoss attitude towards]] [[WeHaveReserves his troops]] was ''scarily'' similar to that of Megatron.
[[folder: Armada ]]
* Why [[spoiler:Starscream's clones have T - Cogs. If you assume that the genetic code he's talking about is equal to DNA, it's completely logical for said DNA to contain code for T Cogs, we would have code for 2 kidneys even if one were removed, the respective genes would just be dormant everywhere but the kidneys.]]
** It's more likely that the DNA simply contains instructions on ''what'' to turn into, and T-Cogs are simply standard equipment in the basic protoform bodies. Simply put, Starscream put software onto existing hardware--he didn't ''change'' the hardware.
** Does this really count as "Fridge"? Because if you ever paid attention in Biology class, it shouldn't.
** However, FridgeLogic ensues when you ask yourself why an alien robot would use DNA as carrier of its genetic information. And on the computer screen [[spoiler: during the cloning process]] a DNA double helix is clearly seen.
*** Humans might just use DNA in the Transformers Universe due to Unicron's influence. My logic for this is basically this: Cybertronians are humanoid, and they showed up first. The original Cybertronians were created by Primus. The core of earth is [[spoiler:Unicron, so therfore he may have been able to influence us while he dreamed.]] Therfore, humans might have been Unicron accidentally mimicking Primus's creation of the original primes while he was asleep.
* Paying attention early on, you'll notice something strange is going on when [[spoiler: the Starscream Clone confronting Bulkhead has his hands change into guns, something that Cybertronians who lack T-Cogs are unable to do.]]
** Even before that, close-ups reveal that [[spoiler:clone!Starscream's scar is missing.]]
[[folder: Tunnel Vision ]]
* Most people watching the show assume that the kids, Fowler and the Autobots simply abandoned Vogel, and...they would be correct. The logical explanation is of course, Optimus was not on location to insist that the man be taken into protective custody. The brilliance on part of the writers is that they took Optimus (the moral center of the team) out of the picture for that part of the episode!
[[folder: Hurt ]]
* Remember in "One Shall Rise, Part 2, when Miko said that Megatron would never forget her face if he hurt any of her friends? [[spoiler:Take a good on Megatron's face when an Insecticon informs him that Hardshell was killed by ''a human girl.'']]
[[folder: Out of the Past ]]
* It was a bit strange that Starscream, who loves EvilGloating (often to his own detriment), would kill Cliffjumper immediately once he was captured in the premiere, instead of interrogating him, or at least making a grand speech. "Out of the Past" shows he had captured Cliffjumper once before. Cliff was about to be killed by Shockwave, but he goaded Starscream into doing his own dirty work. Starscream babbled on for a while until Arcee and Cliffjumper managed to escape. He didn't want to repeat the same mistake.
* This could also explain why Starscream likes to keep bringing up Cliff's death: he was holding a grudge and is just ''that'' satisfied to come out on top.
* In "Sick Mind," Arcee hesitates when told they must enter Megatron's mind via cortical psychic patch to find a cure for Optimus. [[MindRape We now know this isn't the first experience she's had with the patch.]]
* [[Recap/TransformersPrimeS1E1DarknessRisingPart1 'Scream.]] [[Recap/TransformersPrimeS2E17OutOfThePast Been awhile.]]
[[folder: The Human Factor ]]
* In SciFi parlance, a Mech (or more properly, "Mecha") commonly refers to a humanoid robotic machine piloted by a human. What did MECH turn [[spoiler: Breakdown]] into here?
* [[spoiler:Breakdown!Silas]] makes many shrewd errors in judgment, such as [[spoiler:murdering his own men after they seem to have no more use to him]], which could be chalked up to his ego, but is still rather questionable. But within him, you can see that [[spoiler:Silas has a dilated right pupil]], which is a sign of severe brain damage.
* MECH has always been considered to be the human version of the Decepticons. I at first didn't see the resemblance since they are TerroristsWithoutACause while the Decepticons had a legitimate goal of trying to conquer a world to replace their dead one. It wasn't until Silas was put into Breakdown and killed his fellow MECH agents that I realize the parallel between them and the Decepticons, particularly their leaders. Both Silas and Megatron were both looking for weapons to further their goals and stumble upon an even greater and more dangerous power ([[HumongousMecha Transformers]], [[TheCorruption Dark Energon]]). Both try to experiment and harness this power, committing several atrocities in the process (Dissection of Breakdown, [[CameBackWrong Zombie Cliffjumper]]). They both plan to have an army of these toys but were thwarted and nearly killed in the process. They would both also be critically injured in the process, but also be revived by said toys in the end (Megatron is still sustained by the shard of Dark Energon in his chest, while Silas lives on as CYLAS). And they both abandoned their team to appeal to a greater authority ([[EvilOverlord Megatron]] and [[GodofEvil Unicron]]), only to find that they are out of their league. The only difference is that Megatron was rejected by Unicron immediately, causing Megatron to aid the Autobots to stop Unicron, while Silas [[spoiler:was taken to the [[KarmicDeath dissection table]] after he failed Megatron.]]
* Silas thinks he's so awesome now he's in Breakdown's body. But to Megatron, he's just another soldier, with the downside of previously torturing his Sergeant (Breakdown seems to manage the Vehicons a lot) and having all that dirty, short-lived organic stuff inside. If Silas' best gear can't take out a single Autobot, and he can't beat Bulkhead when the guy's still weak, when Breakdown could give him a solid run for his money at full strength, and Megatron risks losing his Medic's full loyalty, and he's trumped by three human children, what use is he?
** Megatron doesn't even care much about ruling Earth - no incarnation ever really did. He just wants to stripmine the place. If we're very lucky he might consider us worthy of living as slaves to assist in the stripmining.
* This is the episode that proves it takes more than a shell to make each Cybertronian. As soon as he sees that body, Knock Out isn't all "Hurray! My head buffer is back!" He barely even mistakes him for Breakdown. He's just disgusted and angry at Silas, a human who's pulled a Frankenstein on his dead friend's body.
[[folder: Alpha;Omega ]]
* When it comes to being evil, the Megatron of this series has gone above and beyond the call of duty. Let's review: He turned against his government, city, and his friend Optimus back on Cybertron - bad enough. Then he destroys the planet in the ensuing war - worse. ''Then'' he [[spoiler: nearly offs someone Optimus is protecting]] - still worse. But ours doesn't quite stop there. [[spoiler: By taking a Prime's arm and using the power of the Forge of Solus Prime, he's essentially telling the Transformers' version of a ''god'' exactly where to stick it.]] Those familiar with what happens before the show will remember what exactly Optimus is: a divinely appointed agent of Primus. [[spoiler: So in "Alpha, Omega", Megatron has offended Optimus's deepest beliefs - and one can tell that Optimus is completely done putting up with Megatron's megalomania.]] If he had any qualms whatever about killing Megatron, they're gone for sure.
** Don't forget shattering sacred relics or the fact that quite literally the only reason he isn't acting as a Herald helping Transformer Satan consume all that exists is because Transformer Satan told him to bugger off. Really, though, he proved his beyond-the-usual-standards evil back in the five episode pilot when he declared that doping with what is quite literally the blood of the devil is a great idea.
*** The frightening part about Megatron and the reason Unicron wanted nothing to do with him is quite simple, Unicron is part of a natural balance between chaos and order and therefore not technically evil, just pure chaos and hate in its most basic form balancing out the base form of order and love (Primus). Megatron is evil in a way more unnatural and perverse tripping up the balance and as such Unicron can't stand a monstrosity like Megatron anymore then his brother would.
** Ironically, this might actually be a continuation of Megatron's defiance against The System, and taking for himself what was normally reserved for the elite. The Primes were flawed, eventually fighting amongst themselves and causing major problems. What would be an even more poetic act of defiance would be if Megatron took the arm of Zeta Prime, AKA, the asshat who instituted the Caste System that enslaved him in the first place. Just because someone was made a Prime doesn't mean they'll deserve to hold the title in perpetuity.
*** The last part is more amusing considering what happens in ''WarForCybertron'' between the two.
* Why did [[spoiler:the [[InfinityPlusOneSword Star Saber]] [[WreckedWeapon shatter]]?]] It's ''ancient''. It's been on Earth for millions of years, embedded in rock, unmaintained and subject to the elements. Cybertronians and their technology need regular maintenance. Most of the other Iacon relics were sealed in special containers. Also, the protective field it generated may have shielded it and the surrounding rock from unworthy Cybertronians, but since it was created on a planet deeply rooted in technology, it probably wasn't designed to keep out nature.
* When Optimus receives the message from the Star Saber, the first thing Smokescreen does is ask if Alpha Trion mentioned him. It turns out that in a way, [[MacGuffinGuy he did]]. Not to mention all that talk about destiny...
[[folder: Patch ]]
* Megatron enters Starscream's mind to decide if it's worth keeping him alive or not. We walk in on Starscream's obnoxious victory dance. The Brilliance? This is Starscream's base consciousness; the factor that his personality is based around. The thing he's thinking about all the time.
* Why did Megatron allow Starscream to stay in the end, despite his, as the former noted, ChronicBackstabbingDisorder? Look at Starscream at the end of the last episode (confident and a SmugSnake) and compare that with him throughout the episode (wimpy and cowardly). The purpose of the psychic patch was for Megatron to mentally break Starscream to the point where he's sure that Starscream won't betray him again.
[[folder: Regeneration ]]
* [[spoiler: Dreadwing dies. But the circumstances under which he dies is suspicious. At the time, he didn't wish to join the Autobots and likewise, he didn't feel like he could keep up with the Decepticons either. Knowing that he'd also have difficulty surviving as a neutral. Let's not forget the fact that he has helped the Autobots by giving them Solus's hammer... which could be seen as an act of treason if discovered which if he turned neutral would have meant being hunted like all the time and eventually dying some day. So he's rather boxed in as to where he could possibly go. In fact, he had no where he could go. Even if he stayed with the 'cons, they would eventually figure out his act of treason. So he had only one option left as to what he could do with himself and that was to go after Starscream to avenge his brother. Now, Megatron warns Dreadwing to stop his assault on Starscream. He was very clear about what would happen. At this point, Dreadwing could have stopped and he would have survived. But he didn't. So what we're seeing on screen isn't Dreadwing's execution. It's Dreadwing's suicide.]]
** [[spoiler: I saw it more as him going out [[HonorBeforeReason the way he would have wanted.]] Though he probably wished he could have [[RevengeBeforeReason finished Starscream]] first.]]
* Why was it that Arcee, of all bots got the Apex Armour? Lets see, ToSellToys would be the biggest reason, if they ever made a properly Apex Armor toy, it'd be easier to have it fit both Starscream and Arcee than Starscream and say, Bulkhead. Secondly, it makes ''strategic'' sense, she can probably run past enemy lines then put it on, use it after a bike-jump, and generally being able to do more than frontal combat.
[[folder: Darkest Hour ]]
* How did Optimus Prime [[spoiler:manage to knock Megatron's Dark Saber hand aside to chop his arm off? He was wielding it with 2 hands, while Megatron only used one. The extra force of his other hand gave him more control on the recoil to give a followup strike right away.]]
* When Megatron starts [[spoiler: cyberforming Earth]], he wonders if "Gilded Earth" would be a suitable new name for it. Now who was the being residing within Earth whose G1 verion was a golden planetoid?
* The Nemesis unveils a surprisingly powerful WaveMotionGun that [[spoiler: splits the Autobot base in half (effectively a small mountain)]]. With the events of "Out of His Head" suggesting the Nemesis didn't have any sort of energy weapon like that, which is why they stole the human made laser lens, where did that gun come from? Well with the recovery of the Forge of Solus Prime and Megatron's vain attempts to use it Knockout suggested they were trying to make a "Fortress Maximus Grade Nucleon Shock Cannon." Megatron used the dead Prime arm to create the Dark Star Saber and nothing else? I think maybe he did.
[[folder: Darkmount, NV ]]
* Why was Jack, normally a pathologically responsible kid, the one to break radio silence and get himself spotted? Because Raf and Miko both have large families (lots of siblings and (effectively) two sets of parents, respectively), while Jack and his mother only have each other. It was Jack's concern for June that led him to contact her, because while the other two know their families will take care of each other, Jack had no such assurances. She's literally all he's got, and vice versa. That'll crack even the toughest shell.
[[folder: Prey ]]
* Ultra Magnus. Why is he so stringent? Well, if he was the autobot equivalent for Starscream, that means he probably had to do all things 2nd's end up doing: watching the troops, and keeping things moving. Optimus might plan, but Magus executes, and when units are worried or tired, sometimes you need someone with a little more push to keep an entire army in check. For all we know, the autobots were a collection of ReluctantWarrior people going into the war, and perhaps Optimus needed a strong military man to balance him since he was a thinker before the war.
[[folder: Chain Of Command ]]
* Miko. Why does she follow Ultra Magnus's orders and respect him, in spite of her showing little respect for authority in earlier episodes? A large part of it is character development- After all, she had been kidnapped by Decepticons and nearly killed, and for a time had literally no idea if any of her friends besides Bulkhead (Who she was with) had escaped safely. However, it also is the fact that BULKHEAD respects Ultra Magnus- The 'bot who Optimus put in charge of the Wreckers, and who Bulkhead greatly admires. (Note that she was also kinda running from Predaking, so she at least has enough common sense to run for help)
[[folder: Thirst ]]
* The Vehicons. While CYLAS did manage to [[spoiler: turn]] a few of them, they showed surprising competence when they were later seen fighting as a unified group against the Terrorcons, more so than when fighting against Optimus and the Autobots. The brilliance comes in when you consider the Vehicons are the ordinary soldiers in the Decepticon army, while all the Autobots with Optimus Prime are usually identified, ranked officers in the Autobot army. In the War of Cybertron, one did not become a ranked officer respected by the ordinary foot soldiers without a great amount of skill. It is not that the Vehicons are bad soldiers: the Autobots are just that good.
[[folder: Evolution ]]
* We see Team Prime chafing under Ultra Magnus' command. While he isn't really a mean guy, his SergeantRock attitude can come off as overbearing. This is possibly why the Wreckers "rusted" when under Ultra Magnus as they weren't used to following his command style.
** Mind, that comment about the Wreckers having "rusted" was made by Wheeljack and no one else. So that may be his personal opinion alone.
[[folder: Minus One ]]
* The episode sheds a new light on Soundwave and Laserbeak's relationship. When Laserbeak uploads his directive to capture Ratchet to Soundwave, he immediately gets up from his self-induced coma and gets to work. This explains why Soundwave was willing to pass up the opportunity to kill Wheeljack back in Triage. Laserbeak serves as a sort of diary. He contains back up copies of Soundwave's data. If the Autobots got Laserbeak, they would have access to vital information.
[[folder: Deadlock ]]
* How is it that only one escape pod was left when Starscream and Shockwave escaped? Because it's more than likely the vehicons managed to escape first. After all, several seekers did leave with them.
* This may count equally under Fridge Horror, but Optimus flies into ''absolute rage'' when Megatron [[spoiler: kills Bumblebee, intent of finishing their conflict and ending his life without so much as a word. Now the death of any of them would have been a heavy blow, but with Bumblebee [[VideoGame/TransformersFallOfCybertron this is something that Optimus has almost seen happen before]], only this time Optimus ''failed'' to save him and Megatron succeeded in killing him (if not for the Cybermatter). He could very well have been having a traumatic flashback to that very moment]].
* Many fans have complained that it was [[spoiler: Bumblebee and not Optimus who finally killed Megatron]]. But Bumblebee wasn't just [[spoiler: putting an end to an evil dictator, he was protecting his leader from suffering a similar fate at Megatron's hands that he himself just barley avoided]].
[[folder: Predacons Rising ]]
* While the Autobots are placing Starscream in the brig, if you look closely at Knock Out you'll notice the gesture he's making. As if he's washed his hands of something? He's symbolically disassociating himself with Starscream, and by extension the Decepticons as a whole once and for all.
* [[spoiler: Why did it take Unicron's torture to make Megatron understand [[HeelRealization the errors of his ways]] this time, even though he has suffered from something similar before, and didn't change? Simply because in those situations, Megatron had fought back against the oppressing force and was nearly successful in keeping Unicron at bay, thanks to his gladiator background. This is why he fell to corruption during the early days of the war. Fighting back with violence and force gave him a SocialDarwinist sense of destiny and invincibility. Unicron's complete DemonicPossession rendered Megtron's willpower and deception useless, making him feel truly helpless for the first time in eons.]]
[[folder: Misc ]]
* We've seen repeatedly that the Vehicons are not simple drones. They have individual voices and personalities. So why are they all [[FacelessMooks faceless mooks]] who have the same alt. mode? Because having a uniform appearance for their footsoldiers makes perfect sense from a military view. And only the higher-ranking officers have the unique names and vehicle modes.
* The choice of a desert town may seem like a simply way to avoid the cost of having to animate trees and grass all the time, but it's not just an American desert state: it's ''Nevada.'' AKA: home of Area 51. The locals are ''used'' to hearing ridiculous conspiracy theories involving aliens and ignoring them, making it one of the perfect places for the Autobots to hide out without causing too much of a commotion. Any news from the area would just be chalked up as more silly rumors by UFO freaks.
* Bulkhead's status as a LightningBruiser. How does the big guy move so damn fast? Well, look at his feet. Specifically look at the ''inside'' of his feet. There's wheels leftover from transformation. It's entirely possible he can use them for bursts of speed when he needs to move faster.
* In addition, it's hinted that Bulkhead's body could be hollow in places, with at least one cavity large enough to accommodate a teenage girl. So he's actually pretty light for a bot of his size.
* The recurring five-note rhythm pattern in the theme song? That's based on the classic transformation sound! The ''Transformers Prime'' theme music is also reciting the "robots in disguise" notes from the original ''Transformers'' theme song.
* A lot of fans have complained about [[spoiler:killing off complex/interesting characters such as Breakdown and Dreadwing. In regards to those particular characters though, it kinda hints at how dark this series ''really'' is overall. The Decepticons with noble tendencies get killed off before the have/get the chance to properly redeem themselves, in both cases by Decepticons with...not-so-noble...qualities, making the faction as a whole a genuine threat in this series.]]
* Most incarnations of Starscream tend to have his design with the color red. In Prime, however, he has a grey color scheme. Most incarnations of Megatron are grey. Starscream is known for wanting Megatron's position as leader of the Decepticons, so the grey color scheme could symbolize him being a "Megatron wannabe".
* Unicron has large horns, [[BeardOfEvil evil-looking facial hair]], and [[spoiler: dwells in the center of the earth, which FluffyCloudHeaven folks perceive as the location of Hell.]] Perhaps he's had some mutually-unconscious influence on human culture...?
* The ''Prime'' human kids are a kind of inversion of the ''[[Anime/TransformersArmada Armada]]'' kids: the respective ethnicities/genders correspond (Jack and Rad are Caucasian, Raf and Carlos are Hispanic, and Miko and Alexis [[AllThereInTheManual (sorta)]] are Asian), but in ''Armada'' Rad and Carlos are the irresponsible ones with Alexis being the more sensible one. Here, we have the girl being the reckless one and the catalyst for the plots of several episodes, with the two boys being more quiet and introverted.
* Bulkhead's toys in the Beast Hunters sub-line have the general colour scheme of Generation One Roadbuster. From a homage point-of-view, it makes sense since Roadbuster, in G1, was a Wrecker, as is Bulkhead from the Prime/Aligned universe...but in this show, Wheeljack mentions how Roadbuster, amongst other Wreckers (also from this continuity) are "all dust." Could Bulkhead be taking on his fallen friend's colours as a tribute to him? If so, [[TransformersShatteredGlass this is not the first Transformers universe where this sort of thing has happened.]]
* The way Arcee behaves toward Smokescreen might come across as unusually hostile as times. However Arcee's backstory involves her first partner Tailgate who was brutally murdered, her subsequent partner, Cliffjumper, follows suit in the series premiere. Watch the episodes featuring Tailgate and Cliffjumper, you'll notice both have very similar personality traits to Smokescreen. The real reason Arcee was hostile toward Smokescreen? She didn't want to become to attached to someone so much like her lost friends, only to feel more pain if she were to lose another like them.
* By the end of the second season, each of the human kids have two Autobot partners in a sense. Jack is friends with Arcee and Smokescreen, Raf with Bumblebee and Ratchet, and Miko with Bulkhead and Wheeljack.
** By season 3 we have Fowler with Optimus Prime and Ultra Magnus.
* The Vehicons going from formidable opponents to mere pushovers as the series progressed could be considered BadassDecay--or it could also just mean the Autobots are getting better at fighting them. Their sluggishness in Plus One is inexcusable though.
[[folder: Darkness Rising, Part 4 ]]
* Megatron's plan to throw Dark Energon through a space bridge at Cybertron to revive the dead as his own army. [[spoiler: Guess what dead gigantic Autobot City-bot is on Cybertron? [[TransformersFallOfCybertron Metroplex]], If Metroplex]] was revived as a terrorcon zombie, the Autobots would be slagged.
** Only Metroplex was placed in ''stasis'', not killed.
[[folder: Predatory ]]
* Given the revelation of Airachnid's...hobby...in this episode, one has to wonder if Jack is the only human she's tried hunting.
** He's probably the first human she's ever hunted, but that doesn't mean he's the first ''[[WouldHurtAChild child]]'' she's ever hunted.
[[folder: One Shall Rise, Three Parter ]]
* Just how many humans died when Unicron came close to waking up?
** Millions? If Hawaii experienced a blizzard, that's thousands right there just from freezing, plus all the tornadoes, hurricanes and the like, there must have been quite the death toll with Unicron stretching.
[[folder: Orion Pax, Three Parter ]]
* Bulkhead states that if the spacebridge crew calls in reinforcements, the odds will be 400 to 1 against the 'Bots. That means there are a minimum of 1,600 Decepticon soldiers ready to fight, not including miners and other servant-class 'Cons. And we know that it's possible to move up in the world and become a fighter. To say the Autobots are outnumbered is the understatement of the century.
** It could have just been an expression. On the other, this does explain why the autobots don't stay aboard the Nemesis longer than they have have to, since every second they spend there is one where the danger of being overwhelmed increases.
** They'd probably have been better off with 1600 Vehicons. Megatron is one bot and he completely curbstomped them.
[[folder: Operation Bumblebee, Two Parter ]]
* When Starscream puts the drop of energon into MECH's prototype, only one of its eyes begins to glow. Why? ''Because they only got one eye when they tried to disect Breakdown.'' Megatron may not be a ghoul, but it seems Silas certainly is.
** No, Silas used the eye to lure the Autobots into a trap and then it got blown up.
** Ratchet put the eye on his tech-reader-whatever-thing, so it was carried away from the explosion when the 'Bots ran. Ratchet probably discarded it after that (the ol' "ew, ''yuck''" *fling* maneuver), which would have allowed MECH to collect it later when they scrubbed the place.
[[folder: Crossfire ]]
* When [[spoiler: Breakdown's]] freshly dismembered corpse is discovered, there's clearly no Energon anywhere. Airachnid is the one who killed him...and spiders tend to suck the fluids from their prey.
** If she had, why would she have needed to find more?
*** She's still...um, leaking(?).
*** So she's a genocidal pedophilic ''vampire'' robot spider. [[SarcasmMode Great.]]
**** Are you psychic by any chance?
** With [[spoiler: Breakdown's death]], this means that [[spoiler: MECH has spare parts]]...
[[folder: Nemesis Prime ]]
* Nemesis Prime's attack on the base must have killed at least two dozen or so personnel.
*** An interesting point: Nemesis Prime seems to have [[spoiler: yellow eyes]]. Who else has them, who isn't in need of them anym- [[spoiler: BREAKDOWN.]]
**** [[spoiler: The eyes did not come from Breakdown, MECH has reconstructed him.... so he can serve as the new body of Silas.]] Whether this is any better is for you to decide.
*** Actually, Silas ends up [[spoiler: having [[AnArmAndALeg what's left of him]] simply stuffed inside Breakdown's corpse and hooked up to his nervous system.]] This is STILL not good news, especially if Energon passed into Silas. AlienBlood in your veins can't be good for your psyche.
[[folder: Armada ]]
* Airachnid, sadistic genocidal maniac, [[spoiler:now has an ''army'' of Insecticons that follow her with absolute loyalty. To put that in perspective, ''one'' Insecticon gave ''freaking '''Megatron''''' a hard time and by the time he finally killed it, he was weakened to the point he was nearly helpless. Airachnid now has an entire ''army'' of the things!]]
** And ''now'', Airachnid's [[spoiler:in stasis and imprisoned by the Autobots, and the Insecticons have reverted to their original setting: loyal to Megatron.]]
** Speaking of the insecticons [[spoiler: most people noted how easily Megatron seemed to handle them when there was a swarm of them heading towards his ship despite in an earlier episode having much trouble with them. Taking a closer look, he wasn't aiming for a kill shot on any of them: he was aiming to take out their wings and let gravity do the rest. He aimed under the carapace of the insecticon and took out it's wings. The Insecticon who fell off of the nemesis was clearly still alive. As for those that landed, they never actually attack him, since Airachnid got trapped in Stasis at that moment, resulting in the above.]]
* The whole [[spoiler: clone and pain]] business in "Armada" was [[CrowningMomentOfFunny played for laughs]], but when you think about it, Starscream basically ''[[spoiler: died]]'' no less than ''five times''.
[[folder: Flying Mind ]]
* Consider that when Knock Out came out of stasis, his reaction to Jack being on the control panel seemed to be "got you now", rather than "what are you doing here", implying he was aware about it the whole time. Consider that the Insecticons, Megatron (who has already demonstrated that he never forgets a face) and Soundwave will have probably been aware of all these organics climbing over them...
[[folder: The Human Factor ]]
* Soundwave still has the picture he took of the kids from the opening mini-series. In this episode [[spoiler:he targets a satellite at the location where Raf was hacking from (and Silas was dispatched to the neighboorhood earlier). That was Raf's house. The Decepticons know where Raf lives.]]
** Addressed in the next episode: Fowler is relocating the family explicitly because of this.
*** Which raises the question: Why weren't Jack and his mother relocated after the events of "Criss-Cross"? Was it just that the stakes didn't seem as high back then?
**** Remember, that was just Airachnid and Silas at the time. Perhaps they thought that with Arcee already studied, and MECH in hiding, it wasn't the same threat level as a whole warship of decepticons.
* Just how much of Jasper (besides the sign of K. O. Burger) was destroyed by the Damocles satellite?
** Given the angle and direction of the beam, I got the impression it shot out over the town into the desert. If not, Fowler's going to be ''very'' busy.
*** They really messed up the part with the beam's trajectory. First of all, turbocharging the satellite's thrusters would send its aim somewhere else on the globe, like, say, Florida or even further to the east. However, in the following moments the aim is seen on Raf's computer circulating the streets, meaning that Damocles is still targeting Jasper from above. Then we have the almost horizontal beam which looks as if Damocles has flown a quarter around the globe (firing all the time!) and when it burns in reentry, it's still in the skies over Jasper. So if it didn't destroy Jasper, it did that to someplace else. Fowler's going to curse the day Silas was born.
* [[MadDoctor Knock Out]] was rather pissed when he found out just what happened to [[spoiler: Breakdown]]. And you know, the episode never really showed just ''what'' [[BodyHorror CYLAS's]] fate was... like [[ColdBloodedTorture how]] [[KickTheSonOfABitch he died]]. [[NightmareFuel Or]] [[AndIMustScream not]].
** In the finale the Decepticons learn that the atmosphere of cybertron was toxic to humans. Given that they now have a human test subject...
[[folder: Regeneration ]]
* Where were the kids when the 'Cons grabbed them? Were they still at school? Where they at home with their families?
** They were probably at school, or at least walking home since the next episode has June calling Ratchet saying that she hasn't been able to contact Jack and he didn't come home.
* Dreadwing was sure pissed that Starscream used Dark Energon to revive his brother. However, Megatron, the 'con he pledged his loyalty to, tried to raise an entire ''planet'' of dead Cybertronians. How would Dreadwing have reacted to ''that'' if he knew?
* More Fridge sadness, but Megatron executed Dreadwing to save Starscream. Considering that Starscream would go on to screw up ''so badly'', Megatron would lose half his army, that means that this relatively noble character's execution, from the perspective of the Decepticon cause, was for nothing.
[[folder: Darkest Hour ]]
* At the end of the episode when [[spoiler:the Nemesis destroyed the Autobot HQ, Optimus wasn't the only one left inside; Airachnid was too. Since her fate is not revealed in this episode, one of three outcomes is possible:]]
** [[spoiler:She may have been blown to smithereens with the base, which is pretty chilling in and of itself, even if it is Airachnid.]]
** [[spoiler:While the base is destroyed, the pod is still somewhat intact, most likely buried underneath the rubble to be discovered by someone/something in the next season.]]
*** [[spoiler: Confirmed. Airachnid's pod is recovered by the Decepticons. However, given she's [[TheStarscream not exactly a loyal Decepticon]], it seems unlikely that they'll free her any time in the near future.]]
** [[spoiler:The impact triggered her release...into a world where she no longer needs to hide herself from the humans.]]
* Megatron planned to use the Omega Lock to Cyberform Earth and destroy all organic life. [[Recap/TransformersPrimeS1E24OneShallRisePart1 But not every lifeform on Earth is organic.]]
* How many people were harmed or killed when Megatron began building his new fortress before Fowler was able to evacuate everyone?
** Darkmount, NV confirms the town was successfully evacuated and left in the dark as to why.
[[folder: Prey ]]
* Near the end of the episode, Predaking gives Starscream a rather annoyed stare after hearing his comments on being a voiceless animal. This is a clear sign that he is a thinking, sentient machine as opposed to a mindless machine. Shockwave has remade Predaking to be completely obedient to his commands. What exactly does that mean for Predaking (and by extension, all Predacons Shockwave revives)?
[[folder: Rebellion ]]
* While it's more of a Fridge TearJerker, Alpha Trion beckoning a dying Optimus Prime to join the Allspark can mean only one thing. When the Iacon Hall of Records was attacked by Decepticons, the ancient Autobot must have perished when it was overrun.
** The guy was an original Prime, practically a demigod. He might have abilities not normal to cybertronians.
*** Besides, WordOfGod on The Fallen, one of the other Primes and also a Multiversal Nexus, is that because they're multiversal nexuses (only one in all the multiverse), they just spend some time in universes where time goes backwards and dying for them doesn't do anything (probably reverting to the concurrent self in the reverse-time universe like reverting to a saved game). He'll be fine, worst-case scenario is he just can't come back to this timeline.
[[folder: Plus One ]]
* Just how many times has Knock Out played '[[LanguageEqualsThought Hide and go shriek?]]'
[[folder: Evolution ]]
* After Ultra Magnus and Wheeljack attack the Predacon lab, Shockwave sets the Predacon containers to drain themselves, then ground-bridges away. A yellow liquid starts leaking from the containers and covering the floor; essentially, the 'bots are stepping in ''embryonic fluid''. It gets even ''worse''. When the containers are half-way drained, the Predaclones start showing signs of life: squeaking, roaring and crying out. They begin to immediately chip away at their containers, all of them desperate to get out. But after Wheeljack ignites the synthetic energon, the whole laboratory is engulfed in a fireball... and during that entire time, you hear the Predacons '''screaming''' for their lives. [[TearJerker Poor little things]].
** As Ultra Magnus stated, if the Predacons got out they would have been turned against the entire planet, with the Humans caught in the crossfire. At the time, they also did not know Predacons could transform, and the resurrected Predacons were Shockwave's attempt to create an army to destroy the Autobots - and eventually the Human race. The choice was between destroying them or letting them live, the latter which would let loose the Predacon army on Earth under Predaking's command, leading to the annihilation of both Autobots and Humans, and eventually the Decepticons. In short, they halted the resurrection of one race in order to save another. At that point, the Predacons were fully grown, so it can't be called "infanticide".
[[folder: Minus One ]]
* Soundwave's actions in this episode paint an entirely different light on the Surveillance Chief's status among the Decepticons. He is willing to place himself in a self-induced '''coma''' to keep the Autobots from getting at vital information, and his ruthlessness in procuring Ratchet once Laserbeak uploads the directive to him is chilling, easily incapacitating Smokescreen and Bulkhead when they got in his way, two Autobots who have bested the other Decepticon officers on regular occasion. Long-limbed, no face, and tentacles he uses when he goes after prey. Does that not make him the Decepticon equivalent of '''[[TheSlenderManMythos The Slender Man]]'''?
[[folder: Deadlock ]]
* Trapping Soundwave in the Shadowzone was pretty clever of the kids. But not so great for Soundwave. He has to roam around the Nemesis as a ghost robot, never able to communicate at all with anyone and when he runs out of energon in his systems, he's going to die a slow and lonely death with no one noticing.
** And just like that, this troper's feelings are crushed even more. The only thoughts I have that because he's such a smart 'Con he'll probably figure out a way to warp himself out by analyzing the last transwarp signals and then trying to do it himself. If he does, there will be hell to pay.
** Considering that Soundwave is a) the show's foremost expert in the subject of Groundbridging save maybe [[GadgeteerGenius Ratchet]] and b) [[OhCrap directly wired into the Decepticon Groundbridge]], I would be very surprised if he wasn't at least semi-familiar with his current predicament (or how to escape from it).
** Or Soundwave will run into Skyquake in the Shadowzone.
*** The Shadowzone has shown to be pretty limiting to its occupants. Re-watch the episode "Shadowzone" and watch the kids run in circles till they are exhausted.
[[folder: Predacons Rising ]]
* Megatron has proven time and again that he is a sick, twisted, and unrepentant sadist. [[spoiler:But after he's freed of Unicron's spark, he orders the Deceptions disbanded and claims he does not wish to put anyone else through what he's just been through ever again.]] With such a drastic change in personality, makes one wonder just how horrible his [[spoiler: torture under Unicron's control must have been.]]
* Near the end of the film [[spoiler: Optimus tells everyone that they've all acted like a Prime and that he has faith in them to carry on without him or the Matrix. But isn't the loss of the Matrix a millennia ago what started the decline of Cybertronian civilization in the first place?]]
** Wasn't the Matrix of Leadership only created when Orion Pax went to the Core of Cybertron and spoke with Primus?
*** Nope, WordOfGod says it was originally created at the same time as the Primes and was what ultimately helped them to defeat Unicron in the past.
* If watching the Autobots reaction to [[spoiler: Optimus' sacrifice wasn't bad enough,]] just imagine how the kids will react when they find out, especially Jack.
* Megatron may have [[spoiler:had a case of RedemptionEqualsLife]], but his situation in general is ''not'' going to be a happy one, even with Cybertron [[spoiler:now restored, with other Cybertronians now likely to return. Most likely, he's going to be on the run from angry Cybertronians (possibly a few alien species as well) for the rest of his life, which for a Cybertronian is likely to be a very very long time]].
[[folder: Misc ]]
* Given the darker tones and the emphasis on the war, TFP could almost be taken as a sort of robotic post-apocalyptic Mad Max. IE A world got to hell over oil (or energy in this case) and the turmoil it might cause.
** Although energon is more crucial, since it's not just fuel for war machines and commerce, but it's also food, ammo, and just about any other logistical need one might care to mention.
*** Not to mention ''blood''.
**** Which makes every their attack (and every single other move, actually) ''CastFromHitPoints''.
* Optimus and Smokescreen may both be victims of a combination of BecauseDestinySaysSo and YouCantFightFate instigated by the greatest mastermind of all: [[spoiler:Alpha Trion.]] Think about it for a moment, who was it that got Orion and Megatronus to speak before the high council where Orion gave his impassioned speech? Unknowningly convincing the council to elect ''him'' Prime and not the one for whom he was defending? Who was it that took the young Smokescreen under his wing when he arrived at Iacon? Not to mention telling the young rookie Optimus's life story. [[spoiler:A way of grooming the next heir to the legacy of the Prime?]] Much of what has happend in the series up to this point can be attributed to a XanatosGambit on [[spoiler:Alpha Trion]]'s part. Meaning that, despite whatever either Optimus or Smokescreen thought, many of there actions were being manipulated by someone else pulling the stings, not a very pleasant thought.
** ...That actually makes a lot of sense. And [[spoiler:Alpha Trion]] shares plenty of similarities, visual or otherwise, with movieverse [[spoiler:[[EvilMentor Sentinel Prime]].]]
** I didn't mean to make [[spoiler:Alpha Trion]] out as the badguy, in a way ''he's'' just as much a victim of fate as Optimus and Smokescreen. Perhaps even more do to being [[spoiler:[[TheChainsOfCommanding one of the thirteen original primes]].]]
* Soundwave is truly the Con's greatest weapon. Shock cannons do damage, but with Soundwave on survailence, ParanoiaFuel is without end, because there is NOTHING he can't pick up. Even autobot transmissions. And judging from what happened with Jack in Season 3, it's all to clear that any slip up in the choices the bots make will lead to immediate exposure.
* There are both Autobot and Decepticon crashed ships, energon deposits scattered all around the planet, tombs of ancient Decepticon warriors, not to mention various random alien artifacts lying around, and an entire graveyard of Cybertronians. Why hasn't a single earthling stumbled upon these? ''Especially'' the ships and dead Cybertronians?!
** Well, the Energon Harvester has been discovered and put in a museum...
** They probably have, but what's to say that they weren't killed in the process, deemed insane or just laughed at?
*** Here's another question, why would the U.S. government allow Skyquakes' remains to stay out in the open for anyone to stumble across? Yes he was ''buried'' but still?
* In the season 2 finale, why didn't Optimus just use the Star Saber to finish off the Decepticons when he had a chance? Obviously, making sure [[spoiler: Jack, Miko, and Raf]] were safe was his top priority, but once they were through the space bridge, there was nothing stopping him from taking advantage of the chaos he just caused by [[spoiler: destroying the Omega lock]] and killing Megatron, Starscream, Soundwave, Knockout, and the rest of the 'Cons present right then and there. Also, after [[spoiler: the Decepticon fortress on earth]] was revealed, why didn't he just use the Star Saber to wipe out the attacking Decepticons? Even the Nemesis is unable to withstand the power of the Star Saber, so there was no reason for Optimus not to make a stand and annihilate the attacking 'Cons. Yeah, there wouldn't be a third season, but there's no in-universe reason not to fight back.
** It is possible that the star saber takes time to recharge before it can use the sword beam again. Thus, Optimus wasn't sure he'd have time to fight back. Also, consider that the cons were essentially throwing EVERYTHING at the autobots at the time. Depending on how they maneuvered, they might have found a way around optimus prime, and taken him down that way. Finally, and most importantly, Optimus wanted to ensure the rest of his team survived, so he wanted to see them off before he tried fighting. He might have expected a ground invasion instead of just a Nuke Em All option, so he wanted that taken care of first.
** Moreover, he could just pull one key out of the Lock and it would presumably stop functioning. Then he would have been able to defeat the decepticons with the Star Saber (now that the children are not threatened by them) and restore Cybertron. Well, maybe the firefight would result in casualties.
** Many modern automobiles have a safety feature where the key can't be removed from the ignition while the engine is running. It's not unthinkable that something as powerful as the Omega Lock would have similar safeguards.
*** Also, there just wasn't time to consider every option. Optimus knew that the longer the Omega Lock was hitting Earth, the higher the casualty count would rise. If he tried and failed to stop the Decepticons once, they'd pile in and kill him, the other Autobots, and the kids. He only had one chance. Destroying the Lock was the one surefire way to stop it.
** It's important to note that Optimus ''did'' use a SwordBeam against the 'Cons when they were attacked on Earth. Immediately after wiping out a wave of them, a second one descended on the Autobots. In short, Optimus simply didn't have the opportunity to fully utilize the range advantage of the Star Sabre's beam attack.
** With the ZergRush going on Optimus knew their best chance was to retreat and disperse (ensuring ''everyone's'' survival) rather than trying to hold their ground in a conflict that had changed drastically in the last 2 minutes. It was a tactical retreat rather than leading a potentially deadly offense. The Star Saber was a game changer in the previous status quo but the fact it was shattered in the second episode shows that even it has its limits.
** There's another explanation for Optimus' decisions: maybe he was just unlucky? Think about it. Optimus had no trouble at all in reclaiming the Star Saber at the start of Darkest Hour; maybe he just wanted to get the kids out of the way (rather than risk them getting harmed in the crossfire)? I think that, had Megs not opened fire on Earth and screwed Prime over, the Autobots would have "won" (keeping in mind that the Omega Lock only grants a ''political'' advantage) after the Lock had been activated. Then, his choice at the end of the episode (i.e. staying behind) may have ended better if the Nemesis hadn't fired a laser into the base. That was kinda unexpected to us too.