Angst? What Angst?: treehugger0123 herself admitted that, from a psychological standpoint, Catherine had gotten off way too easy for what happened to her—if not after her transformation, then definitely after Unmasked. Reboot!Catherine apparently won't be so lucky.
Author's Saving Throw: A JFF conversation between Tempest and KATANA made treehugger0123 realize how morally ambiguous Blacklight's ARGO and Tempest's first meeting was, and almost made Tempest seem like the bad guy for holding an unnecessary grudge against someone who was technically robbed of pieces of himself and only helped White Enterprises by circumstance. Her Reboot backstory makes ARGO's antagonism less ambiguous by having him resort to trickery after his first defeat—not only by lying to Blacklight about Cressolun being a WE base, but dragging WE ships back to Tempest's homeworld of Cressolun to back up his story, thereby directly putting it in danger on two fronts. This makes Tempest's anger towards him far more understandable.
Continuity Lock-Out: There is a lot going on, so you can't just leap in. Averted, though, by the players themselves, who are all too happy to explain who Blacklight is and why the colony had to make peace with him in the first place.
It got so bad that, after the forum was revived, no-one knew where to continue from and everyone just decided to hit a collective Reset Button and start the RP fresh.
Heartwarming Moment: In Platform One, after Catherine's done hearing the invitation to the titular location(which allows the invited to bring one guest), the first thing she does is ask if she can bring all three crew members. She gets her wish.
Portal 2 Spoilers incoming! In one RP chat, A.R.G.O. gets turned into a fried potato and is eaten by a seagull. Him being turned into a potato and getting eaten becomes a minor running gag as far as torturing him goes. In the JFF canon, GLaDOS is said to be his mom, and she suffers a similar fate in Portal 2.
Before the forum shut down, treehugger0123 had planned to give Spectrum and Rainbow a litter of 8 puppies, 6 of which would correspond to the 6 colors of the rainbow and have personalities that matched their colors. Then Inside Out was released a couple years later, and some of the color-emotion pairs matched: Blue—Sadness and Red—Anger. (She also came close with Joy; the cheerful, optimistic puppy is orange rather than yellow, which was given to the timid one.)
When Catherine encounters Adam in Unmasked, some coincidental word choices on Catherine's part make Adam suspect that she is also a telepath. In the Reboot, she's set to gain those very abilities and then some.
The Woobie: Bell would certainly count. She lost her love, and had her legs, flight, and sight stripped away from her. She's been kidnapped, beaten, blackmailed. Azog did all this to her, and while he did die, he managed to inflict multiple stab wounds on her. And YET, she still endures.