Xbolt's plan for the mod is to create a full 36 levels, of various themes.
Currently in the beta stages, Newmaps is still under active development, with Beta 10.5 being the latest release.
Taking place several years after the first Flemoid invasion, the game begins with the Chex Warrior arriving at the general's office, and the general tells him that the Flemoids have invaded again, and that he has to go and zorch them all. After fighting his way through Chex City, the Chex Warrior heads out into the wilderness to shut down a machine that will cover the planet in slime if not taken care of. But after he shuts down the machine, he battles the Ultimus, a rather cheesy looking guy, which results in him getting sent into the Flemoid Dimension. He then fights his way through to the Mutant Cactus, the mastermind behind all the invasions. He defeats it, then gets sent back to our dimension. Nothing has been revealed about the fourth episode, but the final scene of episode III shows Chex City burning, with Flemoids in the foreground.
The secret levels of the game are entitled Idiotic Jones, a parody of the Indiana Jones movies. The first secret level, (E1M9) is plainly titled 'Idiotic Jones', and has little to do with Indiana, other than it is possible to jump across a broken bridge over a pit of slime.
The second secret level, (E2M9) is titled 'Idiotic Jones and the Temple of Chex', and has somewhat more of an Indiana Jones feel to it.
The third secret level, (E3M9) is titled 'Idiotic Jones and the Last Lemonade'. It is a deviation from the standard level formula of shooting Flemoids, and is instead based upon solving puzzles. The puzzles are often deadly in nature. The story of the level follows Dr. Jones as he tries to recover the Golden Cup of Lemonade, before Professor Shmoe does.
An Idiotic Jones IV is planned, but is still a long way off.