The special begins with Woodstock trying to build his nest, but every time, the nest falls apart. Eventually, he decides to tie the straw for the nest in a fancy way, and that time it works.
Later that afternoon, Woodstock's new nest disappears. Woodstock immediately goes to ask Snoopy for help. Snoopy agrees to help solve the mystery, but first he goes into his doghouse, and comes out in a Sherlock Holmes costume, complete with cloak, deerstalker cap, magnifying glass, and bubble pipe. Then, Snoopy and Woodstock go on the hunt for the missing nest.
They first go to Charlie Brown's house, where they wake him up and give him the third degree. He naturally denies having anything to do with taking the nest.
The two then go to Lucy and Linus' house, using an excessive amount of dust to check for fingerprints. Snoopy eventually finds a broom straw, and believes this is enough evidence to make Lucy a suspect. He tries to handcuff her, but she ends up throwing him out of the house.
Next, they go to Marcie's house where Snoopy pulls out his notepad and questions her on the whereabouts of the nest. She is unable to understand Snoopy's dog language so she slams the door on his face.
Then, the two go to "Pig-Pen"'s house, Snoopy immediately dismisses him as a suspect once he answers the door in his usual trademark dusty entrance. As Snoopy takes off "Pig-Pen" responds by telling Snoopy to come back anytime because he does not get many visitors.
Finally, they go Peppermint Patty's house, who thinks Snoopy is playing Cops and Robbers, so she dons a burglar mask and chases him through her house. Frightened, Snoopy and Woodstock escape and keep running until they get tired. After that they go back to the scene of the crime.
When Snoopy and Woodstock get back to the tree, where Woodstock built his nest, they notice footprints leading away from it. The two of them follow the footprints straight to the elementary school. After making their way inside through an open window, they ultimately find Woodstock's nest under glass in a display case, with a title, "Prehistoric Bird's Nest". The two grab the nest and run back to Woodstock's tree, whereupon Snoopy re-installs the domicile for his overjoyed and grateful friend.
The next day, Sally complains to Charlie Brown that her science exhibit has been stolen. She tells Charlie Brown she had a very cool exhibit, and it was a so-called "prehistoric bird's nest". Charlie Brown is able to put two and two together and realizes it was Sally who took Woodstock's nest.
Charlie Brown tries to explain that it was Woodstock's nest, but Sally said it had to be a prehistoric nest, because the straw was tied in an unusual way. When she encounters Snoopy and Woodstock, she demands that they return her nest. The three start fighting for it, Charlie Brown suggests they settle their dilemma at Lucy's psychiatric booth, which she temporarily converts to a courtroom.
The two sides state their cases. Snoopy shows Lucy a document that shows Woodstock is the true owner of the nest, while Sally's case is, "Finders keepers, losers weepers".
After a little thought about it, Lucy declares Snoopy and Woodstock the case winners, so they can keep the nest.
While Snoopy and Woodstock are celebrating, Sally is frustrated that she now does not have an experiment for science class, but Charlie Brown and Snoopy come up with an idea. Snoopy is willing to volunteer to be her exhibit in a re-creation of Pavlov's salivating dog experiment. Although Sally is against it at first, she decides to go along with it, and ultimately gets an "A" on her science project.
As the end credits roll, Woodstock lies on his new nest, it finally gives way and shatters, resulting in Woodstock falling out of his tree.
- Todd Barbee – Charlie Brown
- Lynn Mortensen – Sally Brown
- Melanie Kohn – Lucy van Pelt
- Stephen Shea – Linus van Pelt
- Donna Forman – Peppermint Patty
- Jimmy Ahrens – Marcie
- Tom Muller – "Pig-Pen"
- Bill Melendez – Snoopy/Woodstock
- Peter Robbins - Lucy and Peppermint Patty (screaming only)
This special has less dialogue than others, because Snoopy and Woodstock are the main characters and do not talk.
- It's a Mystery, Charlie Brown on the Internet Movie Database.
- It's a Mystery, Charlie Brown on the Big Cartoon Database.
- It's a Mystery, Charlie Brown on AllMovie.