After Digital Café released Chex Quest 2 in 1997, they announced plans for Chex Quest 3, but in 1999 the company was merged with several others and effectively dissolved, and the project was abandoned. The disappointed fans have attempted to make their own sequel, with rather dubious results (the game heavily relied on resources and content that was "acquired without permission" from other Doom modifications and total conversions), and there seemed to be little hope for an official continuation of the story.
However, in 2008 Charles Jacobi, who was the Art Director and Lead Artist of the original two games, announced on the Chex Quest Fan Forums that he was working on the third episode, motivated by the work of one of the fans on a project called The Ultimate Chex Quest. Jacobi created new art and an entire new episode, and also polished the levels from the original two games (there was an issue with Chex Quest 2 that due to time constraints during production, new art and monsters simply replaced the old ones from the original Chex Quest, making it impossible to combine the two games into one WAD without additional editing), and finally Chex Quest 3 was released. Andrew Benson, the Sound Design Leader and composer from Digital Café, created a few songs for the new episode as well. The game runs on the ZDoom engine (which is bundled with the release) and includes all three episodes, making it an official trilogy. I guess you can replace the first episode currently featured on the site with this release altogether.
Download Chex Quest 3 from Charles Jacobi's website
Chex Quest 3 at ModDB