Dean Jarvis, who is so not the dean who Nancy helped out in the past, calls Nancy to Emerson College to help him with a case. Professor Maszak is a visiting professor from the Soviet Union working with some compound called CLT that someone keeps stealing. He swears it isn't dangerous, but the thefts might ruin his experiment. Nancy agrees to help out and go undercover as a recent transfer student while still secretly hoping that she can spend some time with Ned.
While on the way to meet him, she has a run in with some students when she almost runs over their friend in the middle of the road. She meets Karen, the leader of this group called Protect Our Environment, and Phillip Bangs, an adult she assumes is their sponsor. They tell her that they're rehearsing for a protest they plan on doing when a senator visits campus because he wants to sell off nature preserves and national forests.
Nancy finally meets up with Ned and his friends, and things go well until she brings up POE. Ned suddenly turns all dark and stormy and won't even look her in the eye. When she tries to touch him, he shrugs off her arm and claims he needs to get to class right away. He also blows off plans for their date later that night, and she finds him in the cafeteria with some chick named Angela. It turns out that Angela is on the fence about joining POE, and Ned wants to change her mind. He tells them that he doesn't trust the organization and that he thinks they do things the wrong way.
In the hopes of actually working on her case, Nancy stops by Maszak's office and meets both him and his assistant, Sara. They both seem pretty disorganized and Sara makes a first year chem major mistake of mixing two different chemicals and almost blowing up the lab. Nancy does some research on her own and finds out that Maszak is working on an experiment to use a human growth hormone on different species to help them grow.
Ned gets the bad news that Angela left to join the group and convinces Nancy to go with him to check things out. It turns out that all POE members live together in an abandoned office complex off campus and in some other random abandoned buildings. Karen tells them that Angela decided to live with them and went home to get permission from her parents to move off campus. Bangs randomly shows up and claims he was supposed to leave the day before but missed his flight and Karen was nice enough to let him stay there. Ned finds the whole thing suspicious because Angela's dad actually passed away, so she couldn't get his permission.
Further investigation reveals that someone dropped an earring near the scene of the last theft that looks like a coiled snake. Conveniently, all the female members of POE wear the same thing. While back at the lab, someone hits Nancy over the head (of course) and locks her in a closet before setting the room on fire. Nancy manages to wrap lab coats around her head, break the door down and escape.
While investigating the fire, she finds a hidden door, which the security guard explains is actually an elevator that they no longer use. Nancy uses her lock picking skills to unlock the door and start the elevator, which takes them to an unused basement. Realizing that the thief probably used that as his/her escape, she plans to come back later and check it out.
When she does, she finds tunnels leading to other buildings that the maintenance crew once used. She finds one and follows it almost all the way across campus. It brings her almost directly to the front door of Professor Maszak. He goes off her suspect list though when he tells her that he's trying to find a cure for his wife's illness and he really wants to get a job at Emerson to cover her medical bills. Nancy figures that ruining his experiment probably wouldn't lead to a job offer.
After some more investigating, she learns that Bangs was a professor where Maszak once worked and where someone stole his CLT and some other problems occurred. Even though Bangs told her POE was unique to Emerson, it turns out that there was a branch on that other campus. To make matters worse, someone calls and tells her they have Ned..
Nancy sneaks into a POE meeting and finds out that they are bat shit crazy. Bangs encourages them to take fake guns that look like real guns to the protest with the senator to make sure they get their point across. She keeps waiting for someone to speak up and say this is a terrible idea but no one does. When the talk ends, she manages to sneak upstairs and finds both Ned and Angela tied up and drugged.
Bangs comes in and does the classic villain thing where he confesses everything. He doesn't realize that Karen is right outside and listening. He tells her how he stole the CLT and plans on selling it to the highest bidder. They can put it in any water supply and watch as it magnifies the bacteria of that area and kill anyone who drinks it. When Karen pops back up and threatens to call for help, Bangs turns tail and runs.
Nancy chases him and gets caught in the crowd, but luckily some of Ned's friends see her and help her through. She hops in her car and chases Bangs while noticing someone following her. Bangs goes back to the POE office and tries to attack Nancy, but she conveniently finds a cast iron pan that she knocks him over the head with just as the police arrive. Turns out that another of Ned's friends saw her leave, tailed her, and called the cops.
All is well that ends well. Ned and Angela make a miraculous recovery from their drugging, and Karen asks Angela to help her make POE into the kind of organization that doesn't do crazy things like drug water supplies. Ned asks Nancy for a second chance at their romantic date, and she responds by telling him that they can just order pizza in her room...alone...
*It's funny that when the dean first meets Nancy, he can't get over how young she is. Given that she's helped this college like 900 times already, you'd think he would get over it.
*This is one of those times where the college gives Nancy her own room on campus, which has its own private bathroom. I have no idea how that keeps happening because there was a long, long, long waiting list for those rooms at my college.
*Nancy points out that maybe Amanda didn't tell Karen and the others that her dad died, but I have to disagree. If I trusted some random people so much that I was basically giving up college for them, I would most definitely tell them something like that.
*I have a hard time believing that Ned and Nancy haven't yet done the deed, but they'll probably just eat pizza, play Monopoly, and have a good night kiss before he goes back to his own room.
*It's weird to me that every time she visits Emerson, she's either in a room by herself or with another girl. Even in the late 80s, I'm sure colleges had guys and girls sleeping together LOL.
*Maszak gets an offer of tenure to stay at Emerson, teach, and keep working on his experiments as well as getting health insurance for his wife.
*Despite Bangs being behind the whole thing, he's not even a suspect on the list at the beginning! I hate when that happens! The suspects were Maszak, Karen, and Sara, the assistant who was in two scenes and then disappeared.