The fourth season premiere "Genesis" introduced us to an all-new backstory for lead character Quinn Mallory...but it did so in a very unsure manner. Many fans have cited the "fishy" nature of these revelations and later episodes have built upon what has come to be called "The Fourth Season Conspiracy Theory". Of course, with the departure of Jerry O'Connell, these seeds of conspiracy were never harvested...but it is obvious that the writers left themselves a way to go in either direction.
The most glaring instance which points towards something unusual is the meeting with Quinn's mother in the prison. Besides the obvious doubts Quinn points out, there are some even stranger ones. One oddity is that the Kromagg guards would allow his mother to keep an object sharp enough to pierce flesh on her person. This does not seem at all wise on the part of the guards...unless they wanted her to have it. There is also the shot of the Kromagg commander watching all events as they unfolded in the cell...which means he saw Quinn's mom give him the microdot. Yet, the Kromagg commander did not try to retrieve the dot and was not at all concerned about it when news of Quinn's escape came to him. In fact, the Kromagg commander wasn't concerned about Quinn's escape at all...
The reason for that would later become apparent in Common Ground. In this episode, we discovered that Quinn has the tracking implant which was mentioned in second season's "Invasion". It was also mentioned that the Kromaggs were intentionally tracking Quinn. This all but proves that they wanted him to have the microdot on purpose so that they could follow where it led. After all, the dot was keyed to the DNA of Quinn Mallory...or a double with the same DNA.
During the 1998 DragonCon, I had the opportunity to talk with producer Marc Scott Zicree about this subject. It turns out that the fans were right. The writers had batted around the idea of having a Kromagg conspiracy concerning Quinn's new backstory all the way through the first 12 episodes of season four and they were leaving tracks to keep that path open. You see, their idea was to have Quinn be the unwitting dupe in helping the Kromaggs find the homeworld...it would have turned out that Colin was in fact not Quinn's brother, but actually a modified clone of Quinn which the Kromaggs made from tissue samples taken during "Invasion" (the clone was to have been modified to look different to fit the story). Thus, Colin would have been sent along as a Kromagg mole, ready to pounce once the homeworld was actually found in case Remmy's brainwashing failed to keep the Slidecage open.
Unfortunately, the producers reached an impasse with this in episode 13. They received what was the best idea of the season, "Lipschitz Live!", and an integral part of its story was a Colin double. This killed the clone idea because a modified clone could not have a double...so at that point, the producers decided to say that Colin was Quinn's brother and the backstory was real. Of course, there is still a conspiracy left because the Kromaggs were manipulating Quinn to hopefully bypass his father's Slidecage mechanism so they could invade the homeworld. But, it looks like that is as far as the conspiracy goes. It's a shame really...such a great story comes at the cost of an entire story arc. In a way, it almost goes against the old saying "The good of the many must outweigh the good of the one"...but then again, I really liked "Lipschitz Live!"