Oops, sorry about the delay. Here goes...
The Phantom of the Operating System
This is not quite chronological, it's more thematic - it's the best way I found of grouping/revealing relevant info together.
- Semaphore was not really booted from the Space Police, that's just his cover story.
- His undercover job with the ADU is to locate the source of the dodgy laser swords.
- He suspects the Contralto family, and that there is a link with the ADU.
- He eventually finds out that his suspicions were correct and that not only is the ADU involved, it's really being run by the Contralto family behind the scenes.
- The Contralto family had captured Anderson and Squid man as they were trying to escape Teuthida (after episode #374).
- But why are the Contralto family doing this?
This takes us to...
Planet Cynaptix IV, the Phrankenstynians and The Chandelier Project.
- Of course it's a cover name for some shenanigans!
- The Phrankenstynians are in an alliance with the Contralto family.
- Actually they are using the Contralto family for their own ends and will get rid of them as soon as they are no longer needed.
- Except, it's not the entire Government of Cynaptix IV (#NotAllPhrankenstynians), only Commandant Thalamus and his associates.
- He intends to take over the Phrankenstynian Alliance (their Federation, not actually mentioned in the comic, except for a reference to Phrankenstynian space) and the Federation. Actually, he wants the whole galaxy in his tentacles! He totally said he was going to in episode #442!
How does he plan to do this?
- Using all those people who now have cybernetic limbs and brain implants.
- The Chandelier Project ("Illuminating the Universe with Science") was a giant super computer (most powerful one ever built) connected to the Bigger Dish Network which is perfect for enabling them to trigger a cybernetic army across the Federation (see episode #380).
- Golightly (Eric) is indeed the prototype for this and is not happy about it. He also had access to more than he was supposed to and pieced together part of the plan, but needed help to do anything about it.
Which brings us to...
Felicia and Friends
- Felicia and the other programmers/workers are just innocent pawns (see episode #381).
- The reason Alison was taken out of the picture by Eric was because although she investigated (see episode #443), she wasn't willing to do anything about it (see episode #409, "I've been pretending a lot of things never happened around here lately...").
- Felicia, on the other hand is prepared to get involved and finds out the whole plan with Eric's help (she starts to trust him after he reassures her that he only injured Alison, but that they need to rescue her from Doctor Medulla).
- At this point there is a parody of the musical Phantom of the Opera as Eric fetches Felicia and leads her down through the server rooms to the laboratory (in the basement)
- Golightly is getting more unhinged, though, since he learned Squidman was also involved (unwittingly, on Squiddie's part) and has a plan to wipe them all out and stop the project at the same time by blowing up the servers - to which end he persuades Felicia (without telling her the "blow 'em up bit") to try and hack into the servers from the laboratory computers.
Isaac and Major Tom's storyline
- Major Tom was part of the undercover effort, his job was to get a tracked Space Agency ship into Blacktron Gang hideout (and ultimately Contralto family) hands (see episode #421) - Isaac was the perfect coincidental cover-story.
- Semaphore is helping (Major Tom doesn't know who it is, though). He removes the tracking device to gain trust and he takes the ship to Cynaptix IV, but of course he reactivates it when he finds out the final location.
- Isaac and Major Tom find their way to the Chandelier Project HQ and bluff their way in.
- In episode #431, there is a quip about a dumb mistaken identity plot. Guess what? Yep, there is a mistaken identity plot with Isaac.
- When Eric Golightly escaped to fetch Felicia, he used the axe he'd previous taken. Security are told to arrest the guy with ginger hair carrying an axe. Golightly dumps the axe in a corridor, but Isaac finds it, picks it up and gets nabbed by security (Major Tom gets nabbed too, as an "accomplice").
- As unfortunate as it is for Isaac, it does buy Eric and Felicia some more time in the laboratory.
All of this leads up to a final showdown involving everybody mentioned here, and some people not mentioned, which... I will reveal next week!