Starting at the very beginning, Salvatore Toscanini sabotaged the prototype 'Policenaut' spacesuit to get rid of Jonathan. Joseph Sadaoki Tokugawa, Salvatore Toscanini and Gatse Becker knew that Jonathan and Ed would never have gone along with their plans, being such moral people. Ed alone would never have been able to stand up to them, and so Tokugawa built quite an empire with his legitimate and illegal businesses.
Jonathan's wife Lorraine later remarries, to a scientist called Kenzo Hojyo, but Karen is Jonathan's daughter. There's some problem with Karen, however, connected to the acronym HLA (this could be a reference to haemolytic anaemia). Kenzo works in Tokugawa Pharmacy's R&D department, in the Drug Delivery System labs, so he's well placed to work on new treatments for his daughter, who has to visit Beyond Coast Central Hospital every so often. Thus, Kenzo Hojyo becomes involved in the production of the drug NARC, because he would do anything to help pay for Karen's treatment. Eventually, though, his conscience got the better of him, and he was killed at the meeting on the Wednesday the 15th (the receptionist at Tokugawa's 'Prop' HQ says that Kenzo Hojyo did not leave the building via any of the usual exits). His body was shipped to the Biomort plant on the moon, then brought back briefly to frame Jonathan for his murder. The raid on Tokugawa Pharmacy R&D is a complete set-up, designed to get Jonathan out of the way. Again.
Lorraine was killed by Tony Redwood - acting on behalf of Gatse Becker, if not Tokugawa and Toscanini - as soon as she went to Jonathan for help.
In the 'Flashback' scene where Ed explains how he came to adopt Marc, it turns out that the guy holding the knife was Marc's father, Ridley Redwood, Tony's twin brother. High on Narc, Ridley had killed his wife and was about to kill Marc when Ed shot him.
When you met Tony Redwood for the first time on the shuttle to Beyond Coast, you might have noticed his right hand was bandaged from the wounding you gave him in the alley chase. He proves so difficult to kill because of another of Kenzo Hojyo's projects, K-8. This seems to be a drug which improves strength and stamina, and is used by all Advanced Policemen at BCPD. Redwood is also responsible for the death of Dave Forrest, and is the pilot of the EMPS which Meryl notices is bleeding.
Kris is the surrogate mother of Tony, a government 'frozener'. She was given an artifically inseminated egg, as all 'frozener' surrogate mothers are. An expert in organ transplant, Kris is ideally placed at BCCH to work on harvesting black market organs from the recently deceased, so she cooperated with Tokugawa in order to stay close to Tony. Her parents were killed in a spaceplane disaster, and he was her only family. Tony killed her knowing that she was his surrogate mother.
Tokugawa runs the black market organ network. In space, cosmic radiation causes an increase in organ failures, so "spare parts for humanity" became necessary. The idea was that the mafia would kidnap people on Earth, to be shipped to the Biomort plant on the moon. In return, Tokugawa gave them Narc to sell for their profit.
Narc is a synthetic drug embedded in the K-9 capsules (that is, the shell, not the contents), which explains why Victor found nothing unusual in the capsules Jonathan gave him to analyse. Being a 'Binary Drug', Narc becomes active only after taking 2 capsules. The prototype of the system has part of the Tokugawa crest missing, to show which parts of Narc each capsule contains. This is why Kenzo left a half leaf as a clue. (Out of interest, the leaf is from a black poppy, supposedly killed off on Beyond Coast by the plant virus Viroid S.)
The 'Deep Throat' informant is Jun Ishida, the hunchbacked bloke from BCCH.
Victor Jurgens is killed off during a visit to BCCH, because he found something out, and the bad guys needed to shut him up(1).
Karen doesn't die. It is her reading the news bulletin Jonathan watches on the return trip, but her hair's been cut short (aargh!). She had a bone marrow transplant in hospital and, in a bizarre twist, it turned out that the only compatible donor on BC (determined by the blood sample taken by the doctor) was Gatse Becker. At some point after Jonathan first meets Karen, she tells him that Lorraine only ever loved him, not Kenzo. The package which Ed gives Jonathan in the spaceport is from Karen.
Marc is apparently quite intrigued by Jonathan because he's a smoker. Cigarettes are banned on BC (or, at least, they must not be lit), so Marc has only ever seen them in 20th Century movies, so Jonathan is the first real-life smoker he's ever seen.
If anyone has any additions or amendments, please email me!
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Chris Hoffman (1)