Darker and Edgier: Pretty much established within the first ten minutes of the series, with the savage perma-murder of Cliffjumper. It doesn't get any Lighter and Softer from there, dabbling in themes of terrorism, child mortality, and PTSD.
Death Is Gray: The movie death is alluded to in an episode wherein Bumblebee enters Megatron's comatose mind to find a cure for a disease afflicting Optimus. Megatron is quick to sense his advantage and pressures the scout to agree to a little quid pro quo or else "Optimus fades to gunmetal gray."
Decoy Protagonist: The beginning of the first episode focuses on Cliffjumper, as does promo art and the tie-in comic leading us to believe he'll be one of the main characters. Then Starscream kills him within ten minutes of the episode.
Defiant to the End: Jack, Miko, and Raf were taken hostage by the Decepticons and used as a ransom to the Autobots for the Omega Keys. Each one stated firmly that they are willing to die for the Autobot cause. Optimus was ultimately unwilling to forsake them, but they get a lot of points for being as brave as they were.
Delegation Relay: Arcee, you're in charge... Bulkhead, you're in charge... Jack, you're in charge... Raf, you're in charge.
And also, when the Decepticons begin to lose control of their space bridge.
Megatron: Starscream! What is happening?
Starscream: Soundwave! What is happening?!
Demonization: Megatron does this with the Autobots for Orion's benefit.
When Optimus/Orion asks Megatron why they're called "Decepticons", he tells him that it was a form of Autobot propaganda to demonize them, only they chose to adopt the name as a badge of honor.
Dented Iron: Avoiding the Obligatory Joke, this happens to Bulkhead in season two after suffering serious injuries and being exposed to a chemical weapon. He recovers, just barely, but spends a half-dozen episodes either unconscious or limping around before he is more-or-less back to normal. Even still it was stated (and there are continuing signs) that his range of motion and reflexes will never be the same.
Designated Girl Fight: Largely averted; Arcee and Airachnid have several one-on-one fights and an ongoing emnity, but neither is the designated opponent for the other in group battles (even the Bulkhead/Arcee vs Breakdown/Airachnid fight has them put briefly against their partner's opposite number), and both of them have proved themselves in single battle against larger and more powerful male opponents.
The Forge of Solus Prime is this in the shape of a hammer; with but a few swings you can repair and create anything you want, from T-Cogs to Sacred Swords, even Space Bridges.Even Optimus himself, who even got a nifty upgrade in the process. However, this action drains the Forge of its' magical powers, something Optimus warned was near in the previous episode.
Diagonal Cut: Megatron manages one of these on zombie!Cliffjumper.
Did You Just Punch Out Cthulhu?: Optimus turns the full power of the Matrix onto Unicron's Spark. Either it returned him to stasis or extinguished his Spark outright.
Divided We Fall: Megatron gets wise about this in "Patch". He takes Starscream back despite his self-serving behavior, since he cannot afford to have the Decepticons fighting among themselves if he is to revive Cybertron. In fact, that's what doomed it to begin with.
Do Not Touch the Funnel Cloud: Bizzarely subverted and played straight in "One Shall Rise, Part 1". June's car is realistically dragged by the windforce of a tornado, not the funnel. So is Bumblebee when he tries to hold it still. But June and Raf not only exit the car without being immediately ripped into the sky, but aside from June's ponytail whipping about, it's like the wind is actively ignoring them.
Solus Prime, of the thirteen original Transformers, can be seen using a massive hammer in a Flashback in "One Shall Rise, Part 1". The hammer was later found in "Operation Bumblebee, Part 2" and referred to as the Forge of Solus Prime. Bulkhead proved it can pack quite a punch but it's usefulness as a straight weapon is insignificant to it's other ability; creating virtually anything from raw materials.
Dumb Muscle: Bulkhead knows he is't particularly smart, but no other Autobot has the same raw determination as he does. Bulkhead saves the day (accidentally or not) more often than the others.
Dying as Yourself: Silas winds up combined with Breakdown's dead body, and then as a Decepticon experiment. Then he winds up injected with a combination of synthetic energon—which makes cybertronians incredibly violent and causes them to burn through their energon at dangerous rates—and dark energon, the blood of the cybertronian equivalent of the devil. As you would expect, this horribly mutates him and turns him into a shambling cybertronian zombie who calls out for Energon rather than brains. However, his search for energon causes him to find the stasis-locked Airachnid, who kills him and discovers that its Silas in Breakdown's body. Silas has one last moment as himself before finally dying.
Airachnid: Silas? Whatever have they done to you? More importantly, thank you for freeing me.
Dynamic Entry: An upgraded Optimus Prime does this in "Rebellion" giving Megatron a beatdown and punching him across the room in the same step as his landing on the battlefield.
Eager Rookie: Smokescreen, who was most excited to fight the 'cons when they attacked his station at Iacon.
Earn Your Happy Ending: After centuries of war, dozens of close calls being brought back from death's door, the Autobots betraying their morals a few times, torture, and losing their homes, Cybertron is put on the path to recovery, and Earth is made safe.
Earth Is the Center of the Universe: The current story is pretty minor in scale (The Autobot base is considered to be an outpost and nothing more), but there was a larger conflict in the past. Random things that are Cybertronian in origin do show up quite frequently, but then we find out Earth is actually Unicron, so it might have a bit more subconscious interest to Cybertronians than initially suspected.
Also, it's said that artifacts and Energon were stored offworld during the original war. It could be Earth isn't the only planet this is taking place on, just the only one the camera is on. If Metroplex and Menasor were duking it out over the fate of Gigantion right now, would we know? We don't have much evidence of this now, beyond the fact that the war was quite big and the main cast is quite small.
In "Alpha/Omega", it's revealed that the artifacts were sent to Earth by Alpha Trion, who foresaw that the planet would be the site of a significant battle.
Easy Come, Easy Go: Completely averted due to the ongoing story arc nature of the show. Both the Autobots and Decepticons have been slowly retrieving and stockpiling powerful Cybertronian relics for most of the second season.
Egomaniac Hunter: Airachnid works as a merc to travel to exotic locales and hunt the local sapient lifeforms.
Elite Mooks: Insecticons. While their exact strength varies from episode to episode, they are consistently much more troublesome than the generic Vehicons (such as weaker bots like Arcee and Bumblebee either needing help or using clever tactics when fighting them).
Optimus and Dreadwing vs Starscream, who's wearing the Apex Armor and knocking both of them around with ease.
Energy Absorption: The Energon Harvester can absorb energon from anything, including other Transformers.
End of an Age: Name-checked by Optimus at the end of Predacons Rising as the Matrix being merged with Primus' Core means that the age of the Primes has to end. However, before his Heroic Sacrifice, Optimus notes that each of the Autobots—even Knock Out—displayed qualities worthy of a Prime, and that whatever comes next is merely "the next transformation".
Establishing Character Moment: Breakdown's first appearance has him taunting Bulkhead and being capable of throwing the big guy around. Knock Out's first appearance highlights his vanity, and he even approaches Optimus complimenting the customization on his vehicle mode. Together they were able to briefly take down Optimus himself and subdue the other Autobots, immediately proving themselves far more dangerous than the Vehicon Mooks.
Dreadwing came to Earth specifically because he knew his twin brother Skyquake had been killed in battle and he sought revenge against Optimus for the act. It is this unusual sentimental streak that made him such an unusual Decepticon in the first place, and discovering Skyquake's corpse was desecrated with Dark Energon by Starscream made him turn against his own faction.
Likewise, Knock Out and Breakdown had a very easy, affable relationship that included travelling together. And when the latter was dissected, Knock Out was all too eager to pay back the culprit in kind.
Soundwave is shown caring for Laserbeak, to the point of letting Wheeljack live in order to save it. He is also one of few people who truly cares about Megatron, and possibly one of few people that Megatron may care about.
During season 3, Starscream is shown becoming genuinely loyal to Megatron, only wanting his approval despite what he is.He also grieves for him when the latter dies. He also appears to have a level of care for Knockout, especially in Thirst.
Even Evil Has Standards: Starscream himself has spoken out against Megatron's use of dark energon to create zombies and severely disliked Airachnid for her attempts at undermining his position.
A few episodes such as "Tunnel Vision" and "Hurt" suggest that Knock Out and some of the Vehicons are disgusted by the savage nature of the Insecticons.
Every Helicopter Is a Huey: In spite of the show's otherwise high-tech setting, the only US military helicopters that appear are Hueys. Since the animators could have drawn any helicopter they wanted, one presumes the Huey was selected as they would be universally recognised as "American military helicopters".
Justified in the case of MECH's helicopters as secondhand Hueys would be cheap, easily available and ideal for their missions.
Oddly, despite Airachnid scanning Fowler's Huey for her alt-mode, her appearance in alt-mode is much closer to that of a RAH-66 Comanche, the one and only helicopter that isn't a recognisable UH-1 in the series.
Nemesis Prime, a MECH-built copy of Optimus controlled by remote.
The Dark Star Saber, Megatron's Dark Energon copy of the original. Notably, it's stronger than the original, presumably thanks to its source material.
Evil Takes a Nap: Unicron is in stasis in the earths core, and pretty much has been for billions of years (in fact, the Earth actually formed around the slumbering Unicron). This comes back to bite the Autobots and Decepticons alike in the butt at the end of season 1.
The Decepticons vs. Arachnid's and Starscream's EliteMooks.
The Decepticons vs. The Nemesis/Trypticon.
Evolving Credits: Starting with "Project Predacon", the opening features the updated Optimus, Bumblebee, Shockwave and the Predaking all to a new arrangement of the opening theme.
Exactly What I Aimed At: Optimus and Dreadwing's fight in "Triangulation" ends with them battling at the foot of a glacier where Dreadwing manages to gain the upper hand. Optimus then draws his blaster and fires straight at the face of the glacier just over Dreadwing's shoulder.
Dreadwing: Your aim is poor. Optimus: That is a matter of perspective. The ice falls on top of Dreadwing and buries him.
Extra-Strength Masquerade: The US government manages to explain away a beam of light that creates a giant alien tower and subsequent evacuation of a nearby town as "meteor showers."
Eye Scream: Optimus' plague infection starts at his eye. Breakdown has one eye torn out when he's captured by MECH and left outside as bait.
Megatron gets this in "One Shall Fall" when Optimus knocks him off a cliff, lands on him, and then starts grinding his tires into Megatron's eyes. It was quite epic.
Megatron does this to a copy of Unicron.
Knock Out taps on Breakdown!Silas' eye before having him hauled off for dissection.
Shockwave threatens to gouge out Starscream's eye for his failed Uriah Gambit.
Shockwave: I am tempted to force you to share my perception of things.
Faceless Goons: The Decepticon Troopers, as well as all MECH members shown except Silas.
"Grill" deconstructs this trope when Fowler points out that some of MECH's members could be serving members of the military, hence their masks.
Failed a Spot Check: In "Nemesis Prime" Silas, piloting the titular machine via remote control, climbs on top of the structure he is sitting in, with Optimus following behind. This ends up backfiring horribly, because Optimus ends up smashing Nemesis Prime through the roof, severely injuring Silas. He apparently didn't notice the location of the bots until the roof started to cave in.
Given how the fight was going, he might not have run into this problem, except for Fowler coming in and tricking Silas into a fistfight, keeping him away from the controls long enough to give Optimus an opening. By the time Silas got back to the controls, it was too late.
Family-Friendly Firearms: For the Transformers, this is obviously a traditional and justified case. Averted with Fowler's helicopter in "Darkness Rising, Part 3", which has a Gatling gun. Played straight with MECH, but then again, considering how tough the Autobots and Decepticons are, it's actually justified too. Averted with members of the US Army, who are seen carrying assault rifles but never seen firing them.
Skyquake follows soon after the pilot. He gets his robo-entrails ripped out by Bumblebee before falling several thousand feet to his death. He Came Back Wrong in "Shadowzone"... just in time to be trapped in an alternate dimension.
Tailgate, Arcee'sother dead partner, gets one of Airachnid's talons in the general vicinity of the head. It's not directly shown, but it's still incredibly disturbing to watch.
If you're unfortunate enough to be a Mook in this show, your chances of dying horribly are pretty high. See Family-Unfriendly Violence below for further clarification.
As far as death goes, in "Orion Pax, Part 3" we're treated to a shot of an Insecticon being devoured alive by Scraplets, showing them in far gorier detail than their introductory episode ever did.
Breakdown is positively sliced to pieces by Airachnid. One imagines that one only got through because the animators utilized Bloodless Carnage.
The Insecticons can't seem to catch a break: in "Toxicity", one of them gets shards of Tox-En driven through his throat by an explosion, courtesy of Bulkhead's hidden grenade. You can see him writhing and choking in agony for several seconds before he finally kicks the bucket.
Dreadwing has a gaping hole blasted through his torso by Megatron.
Bumblebee, while trying to to get the Star Saber to Optimus, gets shot three times in the chest by Megatron. They're not shy about showing it, either: we get to see his armor completely melted open and several organs underneath. He then falls into the Omega Lock and is healed and revived, which in turn leads to the example below.
Megatron is then run through the spark with the Star Saber by the revived Bumblebee. He stays on it for roughly a minute as his body shuts down and his optics fade, with this look of utter shock and disbelief on his face all the while. Oh, and the sword itself is clearly stained with his Energon as he slides off it and falls through the atmosphere.
In the finale, it's strongly implied that Starscream is mauled to death by the Predacons. Jesus.
Family-Unfriendly Violence: Despite the TV-Y7FV rating, there are several instances of explicit robot violence. In fact, the sole reason the series is rated TV-Y7FV with all this violence is because these are robots, which serves as an example of Getting Crap Past the Radar.
When MECH was first introduced, one MECH Mook is clinging to Optimus Prime's trailer when he gets hit by a tree branch. The sound the impact makes very strongly indicates that it was a lethal blow.
The Chick: Bumblebee/June. In Bumblebee's case, he's the youngest and most laid-back of the Autobots, while in June's case, she takes to looking after the other humans when the Autobot's can't (including a brief but embarrassing stint as Team Mom).
Fling a Light into the Future: It's revealed that a lot of the Cybertronian artifacts on Earth were the result of those at the Iacon Hall of Records trying to keep special artifacts away from Decepticon hands. But when they receive the Star Saber, Optimus receives a recorded message from Alpha Trion where he said that it was foretold the Autobot/Decepticon conflict would come to Earth and he sent the Iacon artifacts so that they could be utilized by Optimus in the coming battle.
Megatron says this of the three kids should the 'Bots refuse to cooperate. Opening the pods the humans are trapped in will expose them to Cybertron's toxic atmosphere.
Megatron: And then... we can all watch them instantly perish, together.
Foreshadowing: Dark Energon has been confirmed as the blood of Unicron in this series, and Megatron plunges a raw shard of it into his own spark in the second episode, after which he comments that he feels as if he can hear Unicron's thoughts.
A couple instances in "Darkness Rising", in relation to "One Shall Rise":
Megatron also tells Optimus that he would make a "fine Decepticon", which is what happens at the end of the season. (Orion Pax isn't a fighter, having to hide behind the Vehicons whenever anything happens, but is key in deciphering codes written in Iaconian code, having been an Iaconian archivist before becoming a Prime.)
In "Operation: Breakdown", after Bulkhead saves Breakdown, the big guy looks like he's seriously considering joining the Autobots. Then Starscream shows up with backup and tells him to choose right there. He says "Tough break, Bulk'. Maybe in the next life." Breakdown's dead now.
In "Operation: Bumblebee, Part 1", we get a look at Project Chimera, whose shoulders and hands resemble that of Optimus Prime, we learn why 4 episodes later.
In "Sick Mind", Megatron brings up "phase-displacement armor" when talking about why he can't kill Bumblebee. Bee actually gets a piece of said armor in "Tunnel Vision."
In "T. M. I." after discovering that the formula in the data cylinder is the one for synthetic energon, Ratchet muses that it could be used to revitalize Cybertron. It turns out it's been sent by Alpha Trion for this very purpose and later Ratchet himself is the one to use it that way.
Despite the Decepticon belief that humans are primitive and inferior, as well as the occasional Autobot scoffing at the idea of humans posing a potential threat to Cybertronians, the series takes the time to show just how formidable humans can be—often through the kids. Megatron, seemingly having more contempt for humans than any other Cybertronian seen, is not only spared by Jack in "Rock Bottom", and also outsmarted again thanks to him in the third part of the season two opener. So, when his plans are foiled again thanks to a human (Miko, this time) in the events of "Hurt", he finally takes a hint.
Very subtly done with the basis of the kids' relationship to the Autobots and a funny moment in "Regeneration". The Autobots are the humans' guardians. So, naturally, soon after a comedic scene of the kids contacting Ratchet because their rides never showed up after school, scrap hits the fan-blades when it turns out that the Decepticons realized that their protectors were all busy on Cybertron and took advantage of the situation in order to get some bargaining chips.
When Shockwave brings Predaking before Megatron, the Decepticon leader voices his pleasure over him '"tampering with creation yet again."' Two episodes later, we find out that this is not Shockwave's first rodeo in regards to Predacon cloning.
Forged by the Gods: The Star Saber and many of the the other relics were created by Solus Prime, one of the first Cybertronians.
Fossil Revival: Shockwave creates Predaking and the other Predacons by extracting and cloning their CNA from fossilized remains.
Fragile Speedster: Arcee is one of the faster and more acrobatic members of the team, but she also can't take much damage.
Freudian Trio: The Wreckers in season 3. With Wheeljack as the Id, Bulkhead the Ego, and Ultra Magnus the Superego.
Friendship Moment: When things get bad in "Darkest Hour", Wheeljack shows up unannounced and lends a hand. When the others, especially Ratchet, express surprise that the Ineffectual Loner comes helping so readily:
Wheeljack: "We're still on the same team Doc, always will be!"
Fun with Acronyms: The DNGS (Dynamic Nuclear Generation System), a.k.a. the Dingus. Presumably the case with the terrorist organization out to steal it, MECH.
Subverted in one of the tie-in comics. When Ratchet builds a training area for the Autobots called the "Safe," Raf asks if the name's short of "Systems And Firing Evaluation." Ratchet says no, the name just means that it's a safe place to train, but he likes Raf's idea too.
In "Triage" Wheeljack sends a grenade to the Decepticon ship. As punishment for failing to get a relic, Knock Out has to run it out of the ship. Megatron talks casually to Soundwave, then pauses as there is a background explosion, then continues.
In "Patch" memory-Starscream dancing as he celebrates being the Lord of the Decepticons as present-Megatron talks to present-Starscream.