SpawnPoint

Until November 1996, the only registered version of Duke Nukem 3D was v1.3d. They created a new version that had a new fourth episode, and changed the version to v1.4 - Also gave that a new name - "The Atomic Edition".  In order to upgrade customers who had the registered v1.3d CD, they created a patch that could be purchased - that patch was called "The Plutonium PAK".  

In December 1996, they updated it again for a few minor bug fixes, and the version number was again changed to v1.5.  Both v1.4 and v1.5 are "Atomic". The term "Plutonium PAK" refers ONLY to the patch you need to use to upgrade an existing copy of v1.3 to v1.4. (There is a further patch available online for free to upgrade a v1.4 to v1.5).

Using 'The Plutonium PAK' will result on your copy of Duke Nukem 3D becoming 'The Atomic Edition' - The term "Plutonium PAK" refers only to the actual patch.  The resultant game is called 'The Atomic Edition'.   If this is all confusing, your best bet is to forget about the names and use use the version numbers.  :)

In short, if you had the old 3 episode registered version (the registered v1.3d CD), you want to get the Plutonium PAK (and the 1.5 free patch online), and if you don't have any Duke Nukem at all, or just the shareware, you need to buy the "Atomic Version" CD. If you buy the Atomic version, you are done.