After its return, it was sent to the Johnson Space Center in Houston, Texas where engineers went over all parts of the spacecraft, checking and double checking to ensure craft and crew survivability of what was yet to come. After this inspection, it was placed on public display in the JSC Visitor Center.
Apollo 9 was later transferred to Jackson, Michigan and became the crown jewel of the collection at the Michigan Space and Science Center, located on the campus of Jackson Community College. While the collection was impressive, the center proved to costly and the college had to close it and remove the artifacts. Many of them, as well as curator Stewart Bailey, wound up at the Air Zoo in nearby Kalamazoo. Apollo 9 was a sweeter plum sought after by many. Since the spacecraft (as almost all flown spacecraft) is on loan from the Smithsonian National Air & Space Museum, they evaluated the requests and settled on San Diego.
The San Diego Air & Space Museum is located on the grounds of Balboa Park in the Ford Building, built as part of the California Pacific International Exposition, which was held in 1935 and 1936. There it was placed prominently in the entrance rotunda, sharing it's starring position with other aircraft manufactured in California (the Apollo spacecraft was built in Downey, California). The capsule is very accessible, forgoing the plexiglas cover seen on other Apollo capsules. It is displayed without it's hatch, which is sitting nearby.
So after 10 days in space and criss-crossing the US, Gumdrop finally rests about a 200 miles form where it was created. For that, and to celebrate its launch anniversary, Apollo 9 is this weeks' "Spacecraft of the Week'.