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Season 1
- In a way, it feels like they found a way to lock the Warners in the water tower again after the original series ended...at first. Then it turns out the Warners returned willingly, even using Wakko as a battering ram to open the door.
- After Brain spent 22 years shaping the course of the Internet, Pinky states that he went through 22 years of psychotherapy and came to the realization that Brain was abusing him into a co-dependent relationship. Brain merely smacks him and Pinky relapses and says he deserved it.
- Brain spends much of the episode bonding with his robotic son B.R.A.I.N, much to Pinky's envy and confusion about it. Then he finds out that B.R.A.I.N. is smarter than him, and tries to murder him when his father verbally opposes him taking over the world. Brain's Et Tu, Brute? expression is heartbreaking, more so when Pinky blows up the robot by accident. As he mourns, Pinky picks up a broom to sweep up the mess, smiling in reassurance.
- What happened with Chicken Boo; everyone else was allowed to come back, except him. The Warners even have it in their contracts that Chicken Boo could not expressly return because he was the least-popular character, even under the likes of Baloney The Dinosaur, the Hip Hippos, and especially his ex, Katie Kaboom. Chicken Boo snaps, pulls a Face–Heel Turn, and decides to hunt down the Toons that were his former costars so that no one could star in the reboot. (This, irony of ironies, makes him interesting enough to be in the reboot, since he Took a Level in Badass with his disguise game and learned to talk like a human.) Yakko actually sounds sympathetic when asking Chicken Boo if that was his motive, knowing what it was like to be locked away and forbidden. Chicken Boo also agrees when Dot points out that killing the Warners would kill the reboot as well; it was the Toon equivalent of a Suicidal Cosmic Temper Tantrum. Oh, and just as his happy theme song starts, all the Toons he imprisoned break out, all of them out for blood. Hope you've learned to run faster, Chicken Boo.
- The fate of Julia Brain, after she became a politician who refused to listen to Brain's insane plans. Brain mind-controlled her with a chip, and when she resisted, it painfully short circuited her brain, driving her mad. To make things worse, Julia was a compassionate, idealistic Nice Girl, but Brain's manipulations have made her obsessed with revenge against him, leading to a Face–Heel Turn. If the show wasn't a comedy, she'd be a full-blown Tragic Villain.
- Seeing Dr. Scratchansniff in a pitiably unwell condition in his debut appearance on the show. Even the Warners realize they have to make him well again before clowning around with him, because in true good sport, they prefer their prey to fight back as that's more fun.
- In the Halloween special, it is revealed that Yakko's fear is that people don't find him funny.
- Think about it: this fear is so crippling for him that he's the ONLY one of the three Warner siblings that ran the risk of getting his soul sucked out by Nickelwise.
- On top of being terrified of not being funny, he also begins to panic when he realizes he is alone in the building and has no one to talk to. In the original show (and even the revival), he is only ever seen alone for songs or very short segments. It makes perfect sense—Yakko can only do his main shtick to its fullest potential when someone else is there to listen.
- The fact that not only the first thing he does after being rescued is ask his siblings if they think he's funny, but the WAY Rob Paulsen delivers the line. The poor kid is gasping for air and sounds absolutely frantic. He's fine after Wakko and Dot reassure him that they think he's funny and that they're okay, but seeing this vulnerability to the normally unflappable Yakko Warner is pretty heartbreaking.
- Brain's reason for wanting to take over the world: when he was a young mouse, the scientists at Acme Labs chose him for an experiment where a piece of cheese was placed on an electrified plate. Whenever Brain tried to get the cheese, the plate would shock him, leaving him too terrified to get the cheese even after the power was turned off, with the scientists even calling it "Learned Helplessness". After this incident, he decided he was going to be the one in charge one day so he would never have to feel that helpless again.Brain: From that day hence, I vowed I would be the one in control. Of myself, of my surroundings, of the world!
- Also note that baby Brain has a straight, normal mouse tail, but it becomes a bolt-shaped zigzag after he gets shocked twice. His lightning bolt tail is more than just a random quirk: it's a physical scar of his trauma, perhaps one he himself isn't even aware of.
- Pinky's tearful and heartbroken reaction to Drusilla breaking up with him in "Bride of Pinky".
Season 2
- The Warners' sudden deaths in "Please, Submit".
- Pepé Le Pew's cameo in "Yakko Amakko" touches in with how he was Exiled from Continuity from the usual Warner Bros. productions due to Values Dissonance. The way he begs to not be sent to the void to no avail can be a little hard to swallow for the fans of the amorous skunk.Pepé: No! No! Please, mon cheri! Do not erase me! The void! She is cold and dark and--
- Note that Pepé referred 'the void' with female pronoun, showing just how bad it is for him. He's an amorous skunk that hits on female beings, but 'the void' is clearly something he doesn't enjoy with and he's stuck with 'her' forever.
- The part in "Plight of Hand" where Brain genuinely thinks Pinky was killed in the helicopter crash, and starts tearing up.
Season 3
- "Soda-pressed": Despite her cutesy on-stage persona, Gigi Soda is forced by the studio to work all the time and never gets to be a regular kid who plays and has fun. Even all the toys in her house are there for business purposes or merchandise samples she needs to approve.
- In the season 3 finale, Yakko says there may not be a next time as the show's contract hasn't been renewed. Wakko says, "But WHY? I thought people liked us!" and getting Puppy-Dog Eyes. Awww.
- The ending in general: The show’s contract not being renewed, thus most likely dooming the series, is represented by an asteroid about to hit the Earth. And when Yakko tries to comfort the others about the show’s cancellation, Dot points out that they really are about to die. And while the Warners try to think of a good one-liner, the asteroid ends up hitting just before Wakko can say what he came up with. Word of God ultimately confirms that the Warners survive but that is still a bleak way to end the show.
