This story takes place right before the start of Star Wars: The Clone Wars (2008) and shows how the Seperatists took hold of the planet Christophsis. It is, in fact, a prequel.
The music that accompanies the brawl between Rex, Cody and Slick is a variation of the speeder chase from Star Wars: Episode II - Attack of the Clones (2002).
The script originally dictated the start of the episode to involve the clones setting up a combat droid nicknamed "The Beast", similar in design to the dome-shaped mining droids seen in Star Wars: Episode IV - A New Hope (1977). However, to keep the war defined as clones vs. droids and not clones using droids vs. droids, and since the sequence didn't even explain the droid's use, the sequence was cut.
The 'Jedi fortune cookie' message that opens the show reads "Truth enlightens the mind, but won't always bring happiness to your heart."
The trooper with the mismatched eyes who likes to collect Battle Droid fingers goes by the nickname 'Chopper'. The same nickname will be used for the droid with mismatched parts, C1-10P, in Star Wars: Rebels (2014).