Deep in a South American rainforest, animals have been disappearing, allegedly due to the return of a mythical flying beast called Mathra. When Joni's uncle, the famous naturalist Dr. Horace Pythagoras, disappears as well, the ClueFinders are on the case. They are accompanied by LapTrap, who at this point is a Robot Buddy of Dr. Pythagoras. In subsequent games, LapTrap will belong to the ClueFinders themselves.
Setting a precedent that much of the series would follow, it starts off with the kids splitting up. You, the player, follow Joni and Santiago for the whole game, while Owen and Leslie remain at the base camp in order to "be your backup." The rainforest has four areas, each dedicated to a different academic subject. The game begins with the Monkey Kingdom (mathematics) and the Goo Lagoon (logic) being accessible. Your goal for both is to complete a Fetch Quest that will ultimately get you one of the keys to the Lost City. Once you have the two keys, your next goal is to make it through the Jungle Canopy (geography) to reach the Lost City gates. The Lost City itself (science and language arts) is another Fetch Quest, this one dedicated to rebuilding the ancient Mathra trap. Once you've done that, you've saved the rainforest and won the game.
In the year 2000, the Learning Company released The ClueFinders: Mystery of the Monkey Kingdom, a pared-down version of this game that only includes the Monkey Kingdom segment.
This game provides examples of:
- Accidental Misnaming: This conversation, with Who's on First? in the mix.Joni: (in regards to collecting sneeze berries) Listen Bingo.Bongo: Bongo!Santiago: Bongo?Bongo: Bingo!
- Adults Are Useless: Aversion for once. Fletcher Limburger seemed to be able to reach the Lost City long before the ClueFinders did, just not the way the Numerian people intended, as he likely flew over the walls.
- Anti-Frustration Features: Despite that you are intended to solve the problems one by one to figure out which tiles equal which letter in one activity, if you can deduce which tiles will equal a letter based upon another previously correct answer or existing letters (on earlier stages), the game will still allow you to uncover those despite that the given problem does not equal that. In fact, the in-game instruction will mention it's still correct.
- Arbitrary Skepticism: Of course, the existence of Mathra is ridiculous, unlike with all the other fantastical animals that live in the Numarian rainforest. What even is the difference between Mathra and Queen Itchybella's pet Flabberwock? They're both green-skinned reptilian monsters, right?
- Cliffhanger: As the Cluefinders are rowing away, Limburger crawls out of the bottomless pit and vows revenge against the Cluefinders. As hes walking away, the real Mathra emerges and stares ominously at something offscreen.
- Collective Groan: In the opening:Fletcher Limburger: Well... peanuts, anyone?... that's what folks are saying, and there's an old superstition about a monster and a lost city.
Leslie: Lost city?
- Developers' Foresight:
- Going back to the room which houses the key half after you've obtained it will have a golden trinket resting in its place. Joni even has new dialogue if you put it in her backpack.
- The Rings of Fire challenge has dialogue for you loophole-abusing. The game intends you to uncover tiles in a Battleship like way, but it will expect you to do it in a certain order (Based upon the math problems given to you). If you just play it like Battleship and fire at tiles that are "hits" based upon the ones you got correct before, the game will have dialogue for this.
- Early Installment Weirdness: 3rd Grade features more minimalistic animation, bizarro episodes, three full-sized "Worlds" (as opposed to the third act being a rush where you do not have to gather any kind of resource.), and different theme music.
- Establishing Character Moment: Leslie and Owen both get these at the beginning of the game. Owen is distracted from the group's mission by food, setting up his Big Eater tendencies and Leslie remarks that she remembers reading about the lost city their pilot mentioned, setting up her position as The Smart Guy.
- Everything's Better with Monkeys: A whole kingdom of them.
- Flintstone Theming: The Monkey Kingdom is built on puns that combine monkeys with colonial Spanish civilization. The simian inhabitants are called "monkeystadors" (play on conquistadors), and they're led by Vasco da Bongo (play on Vasco da Gama) and his wife Queen Itchybella (play on Queen Isabella).
- I Am Not Weasel: The monkeys refer to the Cluefinders as hairless chimpanzees. Don't ask how a bunch of New World monkeys were able to acknowledge the existence of chimpanzees.
- Interface Spoiler: You can open up the map as soon as you start the game up and can see all three "worlds" in the game.
- Loophole Abuse: Gameplay example. You have to solve the problems to figure out which tiles you had to hit in a Battleship style game. However, if you have a previously-existing right answer, you can simply hit adjacent tiles (Even if they are not the "correct" answer), and the game will accept this.
- Lost World: The setting.
- Mayincatec: The Numerians. Justified, since they're fictional.
- Mysterious Middle Initial: Fletcher Q. Limburger
- Not Using the "Z" Word: Mathra is, for all intents and purposes, a dragon. While he has only four limbs, making him resemble a wyvern, he also exhibits all the major features of a Western dragon, right down to breathing fire. But in the game, he's only ever identified as a "monster" or, occasionally, a "beast".
- Real After All: Mathra.
- Schizo Tech: One can't help but wonder how the "Numerians" built a computer a thousand years ago.
- Seldom-Seen Species: A tapir appears as one of the animals fleeing from Mathra in the "Do You Believe in Monsters?" song sequence.
- Mathra is an obvious reference to Mothra of Godzilla fame. Though he's not a giant insect but a flying reptile, making him more reminiscent of Rodan.
- There is a flower that quotes My Fair Lady, speaking in a cockney accent.
- There's also the talking plant quartet with British accents. They call their swamp home "Liverpuddle". This section of the game has colorful animations and the design of the talking plant quartet as well. They are also the ones to introduce players to beetle bags.
- The guardian of the Chamber of Illusions speaks almost exactly like Rod Serling of The Twilight Zone. It even uses the phrases "picture if you will..." And quotes the show's opening.
- The Flabberwock is a reference to the Jabberwock from Alice in Wonderland.
- Mr. Limburger's name is obviously a nod to Charles Lindbergh. You know, 'cause they're both airplane pilots. For some reason, the U.K. version changes his name to "Lindman." Did they think British kids wouldn't get the reference to an American aviator?
- Trial-and-Error Gameplay: The gate challenges the Monkey Kingdom are very much like this, especially on CHALLENGE difficulty. Oftentimes the appropriate addition, subtraction, multiplication and division tiles will all be visible and you just stand there throwing sneezeberries at them hoping that they're correct. Fortunately, however, if you get a correct letter, you can often figure out where the rest of the ones in the word are and hit them even when the numbers don't match up.
- When He Smiles: Mathra at the end.