This episode is split into two intersecting halfs: The team trying to save a dying Lt. Scott who has been infected with some sort of alien parasite, but they cannot bring him back through the Stargate (similar to John Sheppard in SGA's 38 minutes).
The other half is some strange vision Scott is having of returning "home" with Greer (similar to SGA's Home).
Let's take a look at the really bad part first: While the vision in SGA's Home was the doing of an alien lifeform showing the team something believable and had them find the truth the vision of Scott turned into something far less relevant: A story of him returning home from a unnamed war or conflict zone to marry his highschool girlfriend Chloe. All the other important crew members where there but with totally different roles that had nothing to do with their function on Destiny. Rush as a Pastor. Young as Scott's father and Telford as a Cop.
The only things that kept this segment from looking like a daily soap episode where random black-outs Scott had, that served as a point to cut to the real team trying to save him, as well as him having doubts about all this being real.
There was no fighting to stay alive. No trying to figure out the truth and make his way back to reality. If you cut these vision segments the only thing you would ask yourself would be why the episode was so short. You wouldn't miss this.
So what was the point of that? My guess is that the writers tried to shed some light on how Scott felt about certain people of the crew, but that appears to have been a terrible waste of time. The commanding officer as a father figure? Why not but that was a long time to tell that. Chloe? We already knew they where in love. Greer as his best friend and best man? Sure, I buy that. Still a long time to say it. Eli as Chloes brother? Well from Scotts perspective that would make sense, although I'm sure Eli would disagree. The rest don't really make any sense to me. If this was the whole episode it would most certainly get a 0 or maybe a 1 for Eli as Chloes brother. So let's take a look at the other part that actually did something for the overall story. This is actually something I like about SGU that it always does a little something to push the general story a little bit further. Being stranded on a planet with some killer plants trying to infect everybody with itself and the team trying desperatly to hold a position at the stargate long enough to allow TJ to find a cure for a dying Lt. Scott could actually have turned out to be a pretty good episode (short of the fact that this story has beend used more often). Other then scaring the plants a couple of meters back with flamethrowers they where unable to achieve anything, as the plants couldn't be harmed any other way then by cutting them or by being vaporized by the stargate's vortex.
If this part had been more fleshed out it could have passed as a solid episode but unfortunately it was reduced to a minimum in favor of the negligible vision.
So how does it affect the main story? In Pathogen we learn that Chloe has been infected with "something" by the aliens that once had her captured. "The chair" was supposed to take out anything left behind by the aliens and at the end only Rush knew that it hadn't done that and kept that info to himself as he thought it might come in handy (surprise, surprise). This something Chloe has turns out to make her immune to the plant's infection and by saving Scott with a blood transfer everybody learns that she and now Scott is still infected with whatever the aliens did to her, having Young put them in permanent Quarantine at the end of the episode.
In the end we have 40 minutes packed with a lot of story which is for the most part boring and insignificant. The sad part is that the parts that could have been really interesting or exciting were left unexplored and the only thing saving the episode from being a total waste of time was the unexpected uncovering of Chloe still being infected with whatever it is the aliens did to her. Again this was a long thing to sit through for that revelation and if you were really annoyed by the episode you probably could have missed that.
This season had a very good start with Awakening being one of the most intruiging episodes SGU had so far and then it dipped. Pathogen was mediocre at best and this was probably the worst Stargate episode in a long, long time. When stargate fans wanted a change in how the show was written for season 2 I am fairly certain that this was not what they had in mind. I hope the rest of the season goes back to where it started...