- Awesome Music: The guitar duel between Bob and Megabyte in season 1.
- Badass Decay: Matrix in season 4.
- Bellisario's Maxim: Not everything about this computer world really makes sense as related to how we use computers. It is just an interesting setting, as well as way to bypass fan comments related to the computer limitations. Like "Why are there no shadows?" "Uh...It's inside a computer!"
Hexadecimal: Nevermind, it will be glorious!
- Cliché Storm: Certain episodes have their plot built on a long string of cliches, but it is either done as an Affectionate Parody or otherwise knows what it is doing.
- Complete Monster: Megabyte, an order-obsessed virus, becomes one after season 2. While in previous seasons Megabyte had a personal code of honor and was affable enough to give Enzo a birthday present, after a forced Fusion Dance, he loses those qualities, as shown when he uses an Eldritch Abomination's invasion as a way to trap Bob in an Eldritch Location. With Bob out of the way, Megabyte turns his attention on capturing Mainframe, with the end goal of infecting the Supercomputer and the entire Net. To that end, he lets his sister Hexadecimal get crushed with the side of a game cube, then has her rebuilt with a shock collar so she is forced to power his death ray. He makes it incredibly difficult for Enzo to continue beating game cubes, dooming thousands of binomes to A Fate Worse Than Death and causing untold destruction for the sake of driving the kid into a Heroic BSOD. When he gets into the Central Office, he decapitates Phong and tortures his severed head not only for information, but for his own sadistic amusement. His minions, Hack and Slash, are terrified of him, and he often breaks Herr Doctor's fingers as punishment. Even after being defeated, he's caused so much damage Mainframe can't recover and the heroes are forced to deliberately cause a crash for a chance at rebirth. Later, he returns to Mainframe and impersonates Bob, turning everyone against Glitch-Bob before proposing to Dot and almost marrying her for no reason other than to amuse himself. He is willing to hurt anyone and everyone for his own petty amusement.
- Ensemble Darkhorse: Hexadecimal.
- Epic Riff: The episode dealing with Enzo's birthday sees Megabyte roll up with an electric guitar and play an absolutely face-melting solo. It then turns into a Power of Rock showdown between him and Bob for even more epicness. Megabyte even lampshades how awesome the whole thing is.
Megabyte: "I've always wanted to do that!"
- Epileptic Trees: Quite a few fans like to believe that Megabyte and Hexadecimal merging is what caused Megabyte to become more vile, crazy, and dangerous later in the series. It would certainly explain the stark contrast between "give Enzo a guitar" Megabyte of season 1 and "try to commit genocide" Megabyte of season 3 but that's about the extent to which it makes sense.
- Evil Is Cool: Megabyte. Everything about the character just exudes frightening badassery, from his voice to his look.
- Evil Is Sexy: Daemon qualifies for this. Also Hexadecimal, until her Heel-Face Turn later on.
- Family-Unfriendly Aesop: Little!Enzo tells Infected!Matrix to embrace his hate and use it to defeat Daemon.
- Fanon Discontinuity: Some fans leave out season 4, due to the somewhat disappointing conclusion to the Daemon arc (see Hype Backlash below) and the fact that it, and thus the show, ends on a massive cliffhanger (contrasted with season 3, which gives a pretty satisfactory ending due to the fact that it was originally intended as such).
- "Funny Aneurysm" Moment: Megabyte and Matrix's brutal fight at the end of season 3 makes the earlier moment where Megabyte gives Enzo a guitar for his birthday seem a lot less funny than it originally was. Really, all of Megabyte's antics in the first season become a hell of a lot darker in tone after the later seasons.
- "Talent Night" in general. It's kind of depressing watching Dot plan so much for Enzo's birthday knowing that thanks to unfortunate circumstance, she'd miss getting to see him grow up completely.
- Genius Bonus: The more you know about computer hardware, computer software, computer programming and CGI the more entertaining the show becomes. Several character's names are rooted in technical terminology. In particular the character designs for Phong (phong shading) and Ray Tracer (Ray Tracing) actually demonstrate the CG principles they are referencing.
- There are a few, mostly relating to binomial sequences. The punchline to one joke is told in binary and when Daemon orders Deacon to recite Code 101. He proceeds to recite a series of binomial numbers; the code translates to five, four, three, two, one, zero.
- Daemon's name itself is its own genius bonus. A daemon is a background process which is why Daemon had such a passive process during her infection of the net, simply sitting back and monitoring all of her guardians is her function.
- Growing the Beard: The first two seasons were fun and entertaining, but excessively hampered by Moral Guardians that hindered the growth of a more mature show, they weren't allowed to cut to a commercial with someone in immediate peril (like falling off a cliff) for fear of upsetting the children. The final four episodes of the second season started up some more thematically interesting stories with a continuing storyline that fed through the rest of the series, which really hit its' stride in the first few episodes of the virtually censor-free third season.
- Hilarious in Hindsight:
- Nintendo announced that their next console would be called the "Nintendo GameCube". The fact that the console's default color was purple did not hurt.
Mouse: "Wow! Now THAT'S what I call a bug zapper!"
Dot: "I don't believe it! We've been saved by a game cube!
- Another episode featured a brief gag (aired in 1997) that had a battleship called the SS Cameron catching fire and sinking. This was in reference to the obscenely overbudget fiasco of Titanic (1997) and what people were predicting of James Cameron's career...
- "I am become Gigabyte - destroyer of systems!" - terrifying until you find out there's a computer parts manufacturer with the same name- a creator of systems if you will. Go figure.
- Hype Backlash: The fourth season came out after being uncanceled three years after the third season. With all the Fan Fiction and rampant Wild Mass Guessing from the fandom (with no expectation of ever getting a resolution), there were bound to be a few accurate theories and a few fanfics that proved to be a more satisfying conclusion for the Daemon arc.
- Magnificent Bastard: Megabyte, Megabyte, Megabyte.
- Moral Event Horizon: Megabyte betraying Bob and banishing him from the Mainframe so he could take over. Especially cruel when one realizes that the only reason Megabyte wasn't turned to dust years ago was because of Bob was certain that he could be redeemed.
- Seasonal Rot: Season 4 is not as well-liked as the previous seasons, particularly the "My Two Bobs" arc (originally broadcast as a single TV movie). The fact that it ends on a cliffhanger makes it worse. The "Daemon Rising" arc is liked by some though.
- Seinfeld Is Unfunny: The CGI itself. It was mind blowingly cool when the show first premiered but was still very stilted and awkward because of the technical limitations. It didn't help that Toy Story premiered the following year with a film budget and time table that made some people believe that ReBoot was a cheap, inferior CGI product. This is in addition to the rampant Executive Meddling that hampered the show. The truth is that this show and Beast Wars laid the groundwork for CGI television and regardless of the technical limitations the story and scripting was of excellent quality.
- Spiritual Licensee: Of TRON.
- Squick: The nulls are slimy, multi-colored crosses between maggots and slugs that can make little noise beside a squeaky screech. Aside from Nullzilla which is Fridge Horror unto itself, there's a notable incident where an army of nulls devour one of Megabyte's Armoured Binome Carriers, with two henchmen still inside, and it's gone in seconds. Cringeworthy stuff.
- Stop Helping Me!: Occurs in-universe, practically by name on one occasion.
- In one episode, the Binomes try to win the game for Bob by triggering an Earth-Shattering Kaboom, while still inside the planet. Bob was not amused.
"I'm supposed to save them from the User, not themselves."
- In another episode, when Enzo accidentally lowered the intelligence of everybody in Mainframe, he had to deal with their attempts to "help" when they were all trapped in a game together. Eventually, he discovered the key to victory: Have them "help" the User.
"We are helping! We are helping!"
- Uncanny Valley: Hex's Dot impression in the video game looks right, but maintains or even exaggerates Hex's signature walk with the swinging arms and the sashaying hips. Fetish Fuel turns into Nightmare Fuel when Hex's mask is removed in the form of Bob pulling off Dot's face, complete with squick sound effects.
- In the early seasons Dot especially came across rather doll like, which the creators commented on. Kathleen Barr's fantastic voice work helped minimize the uncanny valley, making her feel more lifelike.
- Unpopular Popular Character: Mike the TV. In principle, could easily fall into a number of scrappy tropes, but he is considered obnoxious by pretty much everyone else in the show. This made his antics skew on the side of endearing to the fans rather than smug goofiness. It helped too that his introductory episode had him rebooting in a game where everyone had to work together to win, and Mike did his part admirably.
- Visual Effects of Awesome: At the time, at least, pretty much every part of Reboot was this. Now, not so much. Several of the models still hold up well though, at least when they aren't moving, and the crazy camera movements proved what an All-CGI Cartoon could do. The Art Evolution of the show is also fun to watch.
- Villain Decay: Inverted. Over the course of the series, Megabyte became progressively more dangerous and went from concocting subversive schemes to eventually taking over Mainframe and preparing an invasion of the Supercomputer. Even when the heroes seemed to have defeated him at last, Megabyte comes back in season four; stronger than ever and completely psychotic, to boot. He's still as vicious and cunning as he was in the past, but now has the ability to impersonate binomes and sprites. Oh and any sense of restraint or morality he may have had before is now totally gone.
- Villain Sue: Daemon. Absolutely nothing short of a Plot Armored Spanner in the Works stopped her plan. No one ever even got to defeat her personally, as her plan required her suicide, and was only stopped after she was dead as an individual but before her infection could destroy the Net.