Greenhouses. Ziplock bag, wet cotton balls and seeds. You can see all the plant parts. This has a printable for the "house". Although I think I might just tape the bags to the window and have a lot of them.
Start with one "magic" bean taped to the bottom along with an invitation to draw what it would become. Lovely! Reading Jack in the Beanstalk together would be a nice rainy day addition to this project.