Artifact of Doom: The artifacts used to resurrect Skeleton King.
Artificial Limbs: Most notably the Robot Monkeys with their robotic arms, which are replaceable. That being said, the writers like to have all sorts of fun having these arms torn, cut, or blown off. There's actually a bit of a Running Gag involving Gibson getting his hand cut off at the wrist.
Aaand it's suddenly subverted when the season two finale reveals that they (or Antauri, at least) are monkeys in Powered Armor. "Continuity? What's that?"
He's channelling power primate energies in the process of temporarily becoming an Energy Being. It's not impossible to surmise that his body reverted to its natural state (what it would have been if he'd not been cyborgified), as he throws off his physical body layer by layer, given that straight afterwards he becomes a spark of energy.
Sprx is usually pretty easy-going, but mess with his friends, and his personality can take a rather scary turn. Take what happened with Mobius Quint, for instance.
Calling him Sparky isn't really a good idea, either…
Big Damn Heroes: Later in the series, The Super Robot pretty much exists to fill this role.
Bittersweet Ending: Season 2's finale, with Antauri's death and Chiro becoming monkey-ish.
Made even more bittersweet in the swedish dub where the series ended after that and was pulled of in such a way that it semmed like an acual ending.
BLAM Episode: Wonder. Fun. Meat. World. Just to name one.
"The Hills Have 5", to name another.
Bloodless Carnage: The Robot Monkeys are common victims of this, sometimes getting their robotic components absolutely mangled while their organic parts usually remain relatively intact.
Body Horror: What happens to people who eat the food from Wonder Fun Meat World.
Skele-Mandarin ends up mutated after being swallowed by the Dark One Worm and living in its stomach for a few months, disfigured by acid and with a claw having grown where his arm had been severed. Horror, indeed.
Bragging Theme Tune: "Super Robot Monkey Team Hyperforce Go! Fighting any evil, they are Shuggazoom's hope! Super Robot Monkey Team Hyperforce Go! Defeating any foe!"
Catch Phrase: The team calls out the show's title before going into battle.
Chekhov's Gun: In Flytor, the titular monster takes a genetic scan of Chiro with its eye. We know this is important because we see Skeleton King in possession of the eye with the scan at the end of the episode, but we're not exactly sure how it will come into play until later in Versus Chiro, when we learn that the eye is entrusted to Mandarin to build a factory to create Chiro clones.
The Pit of Doom turns out to be a prominent Chekhov's Boomerang. The first time it becomes important after its introduction is when it becomes the location of Mandarin's cloning factory. But in the Season Two finale, it's revealed that Skeleton King's real intention for building it all along was to reach the egg of the Dark One embedded inside Shuggazoom to awaken it, hatch it, and unleash it on the rest of the universe. And at the end of Season Four it becomes the place where Skeleton King is resurrected. Phew.
Combining Mecha & Humongous Mecha: The Super Robot itself. Partially subverted in that instead of being seperate vehicles that combine into the robot, it's a super robot that occasionally divides into vehicles.
Collapsing Lair: The Citadel of Bone, with a twist: it puts itself back together.
Disney Death: Antauri. Do we need the tags? Probably not.
Heck; Nova is thrown into a wormhole, Gibson is frozen solid, Otto is eaten, and if Sprx's symbolic death of unwillingly turning evil counts, that makes every member of the Monkey Team guilty of this at one point or another.
Evil Plan: Skeleton King has pulled a good number of these, both episodic small term plans and longer terms plots.
Expendable Clone: A straight example with Chiro's clones, but the idea is played with a bit with Mandarin's. The characters don't treat the clone any differently than they would the original (hell, they might not even be aware he is a clone), but the show itself sure does. The increasingly brutal treatment he undergoes over the course of the plot might have been played a little more sympathetically had he not been a clone...
Genre Blind: The Hyperforce. Seriously. Not only are they willing to simply accept their superficial victories without any suspicions about what the villain might actually be up to, they seem to be gullible enough to blindly believe even the most obviously suspicious characters. This is even Lampshaded by a minor character in Prototype:
Chiro: I know all about you! How you've managed to destroy nearly everything else on this planet! Dr. Takeuchi warned us!
Slingshot: Oh, really? Let's see, were you talking to a human being with a face? Or a disgusting heap of brain on a plate?
You'd also think it would have been a little tougher to get Sprx's love of human women past the radar.
Yet he DOES prefer monkeys deep down, which amazingly only made it more disturbing when it was brought up.
Sprx: Man, you make one ugly chick, Chiro. But if you were a girl monkey... Woocha!
And this subtle one…
Nova: I'm gonna beat the scrap out of you!
The plot of the episode Girl Trouble revolves around Chiro riding around in a small star cruiser with two pretty (and probably older) sisters clad in tight outfits who speak to him in extremely suggestive tones. A "honking" sound effect is heard whenever they move close to him. In one scene, they start to talk to him in suggestive tones again while he is drinking a red-colored soda; he becomes flustered and a GIGANTIC red bubble forms from his nose and pops all over his face. Oh yeah, and Chiro is still in a relationship with Jinmay.
Heel Face Turn: Jinmay at the beginning, and The Sun Riders later on.
Also, the Robo Apes in Ape New World.
Heroic Sacrifice: A non-death related example is in Shadow Over Shuggazoom, when Antauri sheilded Chiro and BT from the giant eye and got himself zombiefied as a result.
Hidden Agenda Villain: Skeleton King. He attempts a lot of short-lived Evil Plans beforehand, but we don't find out what he's really after until the end of Season Two…
Indy Ploy: Utilized a few times. The episode World of Giants is basically one big Indy Ploy orchestrated by Sprx.
Infinite Supplies: Partially averted. The team seems to make routine trips to Shuggazoom's moon in order to harvest rocks to convert into fuel for the Super Robot. They were also shown nearly running out of fuel in one instance and had to stop to refuel at an intergalatic truck stop. Other than that, though, the trope is played pretty straight.
I Was Quite a Looker: Captain Shuggazoom was quite handsome in his days as a superhero.
Killer Space Monkey: The Super Robot Monkeys. Although they're technically the good guys (for the most part), they're pretty relentless when it comes to doing away with their enemies.
Late Arrival Spoiler: "Oh no! Antauri dies?! ...Wait, who's the silver monkey everybody keeps drawing?"
Meaningful Name: Chiro translates to "hero" in Japanese, Sprx uses electrical attacks, Otto is a mechanic and Nova is an explosion caused by a dying star… guess what happens when Nova unleashes her Unstoppable Rage?
Valina does this to Mandarin to make him tell her where Skeleton King's skull is hidden. This is arguably one of the more blatantly terrifying examples, as we actually get to see what she's mind raping him with.
By allowing the Citadel of Bone to be destroyed in an asteroid belt, the Hyperforce inadvertently allows Skeleton King to finally separate himself from it, thus gaining the ability to travel and spread his evil around the cosmos more freely.
No One Could Survive That: Otto says this almost verbatim in one episode, and that's the least of it.
Not Quite Dead: Skeleton King, Mandarin, and quite a few others.
Odd Couple: The most notable are Sprx & Gibson and Otto & Gibson.
Shout Out: If you look closely, i.e., Chiro's uniform is exactly the same one that Joe/009 wore in the first Cyborg 009 series, the black and white one.
Not to mention that the reborn Skeleton King bears a striking resemblance to Darth Vader.
The sound effects inside the Super Robot are straight from Star Trek.
The Black castle rising up, in the last episode, looks remarkably similar to the ending of Viewtiful Joe 2.
So Last Season: Black monkey Antauri being reborn as a much more powerful silver monkey during the start of season 3. Face it, he looks so much better in silver.
Speaks Fluent Animal: Chiro was the only one to understand the monkeys at first.
Spider Limbs: Antauri gets these as the Silver Monkey.
Spider-Sense: It's not an epsiode of Monkey Team unless Antauri starts at least one of his lines with, "I sense..."
Start of Darkness: When the Alchemist turned into the Skeleton King.
Stalker Shrine: While exploring the Citadel of Bone, Gibson and Chiro come across a room filled with Chiro's childhood possessions, including his grade school uniform. The following exchange takes place in response:
Gibson: Well, that's extremely disturbing.
Chiro: Tell me about it.
Status Quo Is God: Maybe in the first two seasons, but after I, Chiro? A-VERTED. And now that Antauri is the silver monkey, we'll never forget it.
Of course, the status quo might actually be the Hyperforce's perpetual battle against Skeleton King; Sprx even points out that SK always manages to remain a threat one way or another, even when he's not actually alive.