Yorphius II by KeenRush was the first full Commander Keen 1 mod. It was released back in early 2002. A deluxe edition with more polished graphics was released by Tulip last year, almost 12 years after the original. The deluxe version also features AdLib music created by Paramultart.
A sparse but to the point modified story text accesible from the main menu explains that Keen's pet yorp Spot (a one-eyed green Martian from the first Commander Keen episode) has been captured and taken to Yorphius II, the home planet of the yorps. Keen must find four "activators" (modified ship parts) to open his cage and save him.
No modifications had been made to the overall engine in terms of enemy behaviour, physics, etc, as patching had only just become available at the time of its creation. In fact, the changes were originally made directly to the EXE file. Since then, mods have typically used a program called CKPATCH to modify the game once it is loaded into memory.
Yorphius II is moderate in difficulty but does require some refined reflexes and therefore good experience of the original game. Expect some blind leaps of faith jumping off the bottom of the screen into the unknown, though it is far more forgiving than some of KeenRush's later mods.