Initial copies of the 25th Anniversary Edition are packaged in a metal tin. Inside the tin is a carboard box/sleeve with four individual slim DVD cases, each with individual episode-specific artwork. Also in the package are four mini-posters that utilized the same artwork as the DVD cases. Subsequent re-releases eliminate the tin.
In addition to the four new-to-DVD episodes typical of these sets, the 25th Anniversary Edition contains two bonus, previously-released episodes that cover the transition from Joel to Mike. These appear on disc five and are housed in the same slimline case as disc four.
- Episode: Moon Zero Two
- Extras: Introduction by Hammer Films Historian Constantine Nasr, Return to Eden Prairie, Part I: The Crew *, Theatrical trailer
- Episode: The Day the Earth Froze
- Extras: Return to Eden Prairie, Part II: The Locations *, MST Hour wraps, Theatrical trailer
- Episode: The Leech Woman
- Extras: Return to Eden Prairie, Part III: The Characters *, Life After MST3K: Mary Jo Pehl, Theatrical trailer
- Episode: Gorgo
- Extras: Ninth Wonder of the World: The Making of Gorgo * (MST3K Edition), Leonard Maltin Explains Something, Theatrical trailer
- Episodes: Mitchell, The Brain That Wouldn't Die
- Extras: Last Flight of Joel Robinson, Interview with Marilyn Neilson
* A Ballyhoo Motion Pictures documentary