This time, danger has come to the kids' own hometown. While retrieving a frisbee from Miss Rose's overgrown garden, Joni and Santiago are suddenly swallowed up by the earth. Leslie, Owen, and LapTrap journey underground to rescue them. It turns out there's a whole civilization of sentient plants down there... and they're preparing to go to war with the surface!
Fortunately, there's also a friendly plant named Ficus, who serves as your Exposition Fairy. He tells you that you need to sneak into the throne room in order to gain an audience with the plant leader. To do this, you have to build bridges over three Bottomless Pits. Wouldn'tcha know it, this involves a Fetch Quest in which you collect the bridge planks that are scattered across the plant empire. Once you do make it into the throne room, you'll have further tasks to complete in order to stop the invasion and save the town.
This game provides examples of:
- Artistic License – Botany: The whole concept of an underground plant civilization would seem to ignore the fact that plants need sunlight for photosynthesis. Yes, these are sentient, talking plants, but they are still green plants, and the entire reason that plants are green is because of the chlorophyll used in photosynthesis. Weirdly, some of the educational content actually discusses photosynthesis, but this apparently doesn't apply to the story's logic.
- Artistic License – Law: "We humans have laws against polluting the environment." And once the polluting factories have been identified, they are apparently shut down immediately. Realistically, that would probably take months or even years of legal action.
- Beneath the Earth: The setting, occupied by the titular Plant People. Visitors beware—it's also a Fisher Kingdom of the "physical modification" type, slow-acting but thought to be permanent.
- Body Horror: The Transflormations from human to plant person. When it happens to Joni, Leslie actually truly falters in her resolve to complete her mission.
- Broken Bridge: You very literally have to build bridges in order to advance the story.
- Chekhov's Gunman: Miss Rose appears in the prologue, saying her greetings to the Cluefinders. Later, Leslie finds her cane and worries that Miss Rose was kidnapped as well. It turns out Miss Rose was the plant leader, and she explains that she's leading the invasion to save her people.
- City with No Name: The ClueFinders' hometown is never referred to by name. Mostly, it's just called, "the town." The Incredible Toy Store Adventure! would later establish that they live in San Francisco, but there's no hint of that here. If anything, this game gives the impression that they live in a mid-sized town.
- Continue Your Mission, Dammit!: Owen and Leslie will talk about how you are taking awhile during one challenge. But it's a reading comprehension challenge... come on guys, really?
- A Day in the Limelight: This game marks Leslie's most prominent appearance in the series. The kids almost always split into co-ed teams, and you're nearly always with the team that has Joni, whether she be paired with Santiago or Owen. 6th Grade is the only time you spend the entire game with the team that has Leslie on it. (Not counting 4th Grade, in which the kids don't split up).
- Foreshadowing:
- Before you "officially" get the clue about the plant kingdom being polluted, the "Recipe for Disaster" activity has you feeding toxic chemicals to a plant guard. If you click on Leslie during this activity, she'll comment on how strange it is that these chemicals are down here.
- The game's opening shot, with Joni catching a frisbee, has a polluting factory in the background.
- Gaia's Vengeance: The plot comes about because of waste dumped in the water supply.
- Gender-Concealing Writing: Prior to the reveal that Miss Rose is the leader of the plants, the plant leader is never referred to with pronouns.
- Heroic Sacrifice: Joni pulls a non-lethal one off when the leader of the plant people Miss Rose demands a hostage to stay behind to ensure that the humans' mission to clean up the plants' water supply goes off without a hitch; she immediately volunteers, citing that Santiago's the best choice to investigate pollution sites and that Owen and Leslie knows their way around the underground. She remains calm and trusting in her friends even as she turns into a plant person.
- Herr Doktor: Dr. Fern speaks with a German accent.
- Hollywood Darkness: The underground setting seems to be quite well-lit, despite there being no apparent light sources.
- Hyperspace Arsenal: Somehow, Leslie can carry around six bridge planks at a time in a backpack that looks too small to hold even one.
- Interface Spoiler: Owen's Continue Your Mission, Dammit! will come off as this, unless you saw a scene that could be missed by using the Warp Whistle earlier.
- Later-Installment Weirdness: This game features a lot of CG, only two "worlds", you control Leslie and Owen the entire game (instead of just at the end), the second world has only Santiago giving hints, and the backpack makes a completely different noise.
- Multiple Head Case: You have to knock out a three-headed plant in the "Recipe for Disaster" activity.
- Permanently Missable Content: If you rely exclusively on the Warp Whistle to get around, you may end up missing some of the Cutscenes.
- Plant Person: It's right there in the title.
- Plummet Perspective: When you're building the bridges over the bottomless pits, there's a recurring animation of a rock falling.
- Prevent the War: The goal of the game is to prevent a war between the plant empire and the human town.
- Reasonable Authority Figure: The plant queen, aka Miss Rose, is revealed to be this. While capturing humans as part of her invasion, she spares the Cluefinders from being turned into plants and explains that her people are actually dying. She took the identity of Miss Rose to find a peaceful solution and feels that invasion is the only way to save the plant people. When the Cluefinders say they'll help her stop the pollution if she halts the invasion, Miss Rose agrees. When taking Joni as a hostage to ensure their cooperation, and with Joni's permission, she makes sure to reverse the plant transformation when the Cluefinders stop the pollution.
- Recycled Soundtrack: The game reuses some tracks from 5th Grade Adventures.
- "Shaggy Dog" Story: The first part of the game is all about getting into the throne room the back way. As Ficus repeatedly tells you, you can't go in the front way because you would be captured. But when you do finally manage to get in the back way, you're immediately captured anyway.
- Token Heroic Orc: Ficus, for most of the game. He does say that he has friends who share his views, but we never see them. Also, it turns out in the end that the plant empire isn't really evil in the first place.
- Transflormation: What happens to Joni while held captive.
- You Will Be Spared: Because they were polite to her and the heroes of the town, Miss Rose doesn't turn the Cluefinders into plants after she captures them. This applies to Joni and Santiago, who remain human while trapped underground. Then she explains to them that the plant people are dying from the pollution and they're invading the town out of desperation to survive; Miss Rose is willing to negotiate for another solution. Joni only starts becoming one as a hostage, but Miss Rose turns her back once the Cluefinders solve the problem, reassuring them that Joni just needs a long rest and she's physically fine.
