Third Party Scenarios, or simply scenarios, are fan-made projects, like a new game in the Marathon series, but then unofficially. 3rd Party scenarios are distinguishable in total and minor conversions.
Minor Conversions are scenarios more based on the original trilogy. They usually have changed physics, shapes, textures and sounds, but not as much to completely replace the original trilogy. The story, however, can be completely different and may not even have anything to do with the Marathon series.
total Conversions are scenarios that have very little in common with the Marathon Trilogy. They usually have completely new weapons, items and monsters. They can also contain improved versions of already existing monsters (like the wasp and looker, both included in Marathon: Rubicon.