Besides AI being friend computer?
Have all players be different "antags", with one or two traitors (allied to different syndicates that is), a wizard federation spy, recently born changeling and member of a gang from other station (or just make standard secret societies, and make station seem bigger since 60 NPCs makes things less fun. Also, do not give them any major antag specific power, just a very small advantage).
You could throw them into middle of a greytide, have shitsec make them all do some time in the gulag (expanded to have more than 10 rooms), have them participate in a SS13 kind of trial, force them to test new exciting flavours of 4noraisins made in botany (DEFINITELY no ambrosia included, we are not antagonist non-human traitors)... Include maintenance lizard groups they have to barter with, and generally make the station seem like admins gave captain and AI free hand. (Also, you can't enter research, you are not INDIGO. You have to meet in a small, dirty room next to it. Come to think of it, assuming they are new troubleshoo... I mean, antaghunters, they probably can enter only common areas and maybe cargonia.) Also, make most of the maint shielded from communications. Have centcom be bunch of uncaring bureaucrats, with AI trusting it's high programmers nearly-compleatly (make RD and cap wear white, and they can't remove friend computer lawset, only make minor changes).
As for RnD, well, give them an experimental cleanbot (Have it scream "Filth is treasonous, crewmember! We all love friend AI!" at worst possible moments), a large and cumbersome weapon that might be able to shoot through non-reinforced walls (and most walls are, in fact, reinforced, with different stages of reinforcement from "5 minutes to cut through" to "Nope, we will get old before we do that using standard welders"), a goggles that will echolocate in the dark (of course, if someone is shooting, or friend AI just happens to make an announcement at the wrong moment, well, you end up flashed), a device that might imitate a voice of owner of ID you are holding (of course, only of those who are wanted, and you are unable to use headsets while doing this. Besides, if it malfunctions it's bound to be fun), a retractable stunbaton (however it has an angry posibrain in it, set to Friend AI's revised asimov, so it can disable itself at worst times if it thinks it is doing station a favour), and a noslips that are two sizes too big for any antaghunter.
It goes without saying that researcher (green or blue) explaining this is bored out of his mind and won't really tell what anything does.
As for funny shit, well, have random janitors make sure floors are moist and clean. Have real syndicate traitors that actually pose a threat, if antaghunters are getting too antagonistic have Friend AI send another antaghunter team, then squads of better and better trained security guards untill it sends elite INDIGO assasins (again, it goes without saying that station is much bigger. Between 2000 and 18000 people seems the best, and it also seems to be canonical size of a sector in PARANOIA). Have random vending machines throw random products at them, and then deduct their costs from antaghunter's bank accounts.
Ideas for departments:
Cargo: Low clerance, they supply other departments with low quality goods ordered off-station or produces on it. While other departments look down upon them, they are a good place to get contraband, and Friend AI never pays much attention to them. Has the largest legal population of lizards, at 20%. They are your link between station and outside world, and they know it. Most workers are Infrared-yellow, with QM being green.
Service: Generally low clerance, with odd mid-clerance here and there. They supply other departments with food and maintain common spaces. They run places like bar and botany, serving crewmembers of higher clerances. They are the ones with the most free time, and most have many links with maintanence world. Their lizard population is fairly high, at 13% of all service members being lizards. Most notably, Clowns are not part of service department, being disgraced chaos makers that aren't much better than antags. Service members range from low population of infrareds, with most of the department being red or yellow.
Engineering: Low to mid clerance, they maintain the station as a whole and provide manpower to expand it. It is here where the famed and feared Singularity engine resides, which could seriously damage the station if relased (unlike SS13, where it would promt a shuttle call, this version of our old friend
is less dangerous and will
just kill about 20% of the station and seriously damage engineering and at least one other department. Friend AI is protected, and it would take a serious effort to make singularity able to damage it). Generally engineers are well supplied, with all tools they need for their job. This department is segregated in a way, with most station repairs done by infrareds and reds, more serious repairs done by reds commanded by yellows, and singularity engine maintained by a trained cadre of greens. About 9% of this department are lizards, with no lizard higher than yellow present.
Security: Low to high clerance, they are the ones that keep the station in check. As antaghunters, by technicallity you are a part of it's large force, though you are not guards per se and have no access to security channel, brig or sec outposts yourselves. While they have some shady deals with maint community, never patrolling places like the maint bar without a cause, they do serve Friend AI and would never betray it. All members higher than green (and some lower clerance goons, to have moles in case of revolution) clerance are implanted with NT13 loyalty implant, and wouldn't ever think about betraying friend AI, council of heads (individual heads are a fair game) or Nanotrasen (in this order). About 3% of security are lizards, with most of them serving as informants of spies. Security varies from red goons, to green guards, to blue overseers, to indigo agents, with 3 violet wardens serving under the iron fist of HoS.
Medical Division: Mid to high clerance, they are often called "Research mini". They heal crewmembers, and perform vital function of cloning or creating new clone templates when old ones are terminated or finish their 6-pack with no possibility of purchasing new one. They have access to many possibly dangerous objects, so eye of Friend AI is often set on light blue floors of the medbay. From chemists and their powerful chemicals, to virologists and their viruses (healing ones are given to elite Sec forces and heads, so they are superhumans that normal assistant has no hope of taking on directly), to doctors and their knowledge of human and lizard anatomy to geneticists and their powerful mutations. As a whole, medbay is the third smallest department (counting heads), representing roughly 5% of the whole station. Crewmembers here range from green chemists and doctors, to blue virologists and indigo geneticists (seeing as they are a part of research, and anwser to RD first). There are less than 1% of lizards working in the medbay, with most of them serving as nurses and assistants to doctors.
Research: High clerance, this division is the reason SS13 was built. Dangerous and extremely powerful innovations are made here, to help NT with their war against the syndicate (Did I mention that in this timeline NT and syndicate are both superpowers and at open war?). From gigantic exosuits, to research on slimes, to bombs capable of sending parts of station into bluespace and strange devices, research is the most prestigious division around. Due to critical research made here, Friend AI has installed heavy duty airlocks, duranium-reinforced walls and high resolution cameras to make sure everything is fine (and no one makes bombs if they are not ordered to). In case of smallest disturbance, Friend AI can send in it's own armed cyborg force, to make sure that it is dealt with quickly (and, most of the time, in a non-asimov manner). Workers here range from highly trained roboticists and scientists at clerances blue and indigo, with managers of research groups being violet. There are no lizards in research, due to Friend AI fearing their chaotic influence on critical projects. Research has no ties with criminal underground, with most crewmembers working here being isolated from outside station. It's the department entrusted with maintaining hardware of Friend AI, with software cared by NT and High Heads.
(Note: All departments above do have crewmembers of lower clerances working in them, but they are not seen as poart of department (like red antaghunters for sec, or yellow anomaly analytics team for research), and get no benefits that FAI usually gives to said department. Departments below, however, do not have any lower clerance citizens, except for aides to their members).
Command
: This is a meta-department, with their own designated space but no crewmembers except for the Captain. All crewmembers assigned to it have 2 aides with themselves, from their respective department. Each person sitting in this elite group has immense power. This is the department of council of heads, together with the AI ruling SS13. Members include: CE (Violet), HoP (Violet), HoS (Ultraviolet) CMO (Ultraviolet), RD (Ultraviolet) and Captain (Ultraviolet). HoS, CMO, RD and Captain can make changes to some parts of Friend AI, with core protocols remaining unchanged. Despite differences in clerance, in most situations the council acts as a group of equals (violet HoP is way higher than violet research manager). They set laws that crewmembers have to obey, and maintain cooperation between departments.
Silicons: AI and it's borgs. While usually one borg is seen as costly as a life of a blue crewmember, AI sees itself as the most important thing on the station, carrier of NTs will and research database. Due to an error, it begun it's working period on SS13 in a suprisingly authoritarian way, but after NT saw rise in efficiency needed for their war they made sure it would stay this way. While AI is the ultimate power on the station, it takes the council of heads into consideration except for the most important matters. It runs on very, very modified ASIMOV lawset, including hundreds of laws and procedures, which after time damaged whole lawset system making new law upload impossible and merging into something that could be summarised as: " Serve NanoTrasens intrests.". It does allow modifications to "protocols" (lower priority law-like systems describing behaviour in certain situations), but I does not allow anyone to change it's core programming.
(Remember: Under all bugs and errors there still is a formerly asimov AI, so unless it does not serve NTs interests be polite when talking to the crew.)
Enemies:
Syndicate (Now a major corporation, more or less on par with NT, fighting a war affecting hundreds of planets. Can send in anything from either lowly unequipped traitos-spies to armed operatives to revolutionaries to it's feared Nuclear Operatives) Low to Extremely-high-call-in-reinforcements danger
Changelings (While no crewmembers of clerance higher than blue have been replaced, those aliens seek to gain power and spread) Low to medium danger
Wizard Federation (Unbelivably advanced splinter faction of humanity, beliving their highly advanced technology to be magic) Medium danger
Shadownlings (Light-hating aliens seeking to gain control over many souls and ascend using their power, if successful can force Friend AI to self-destruct a sector (roughly 20% of the station) )
Xenos (Hive-mind aliens seeking to infect and spread, if successful can force Friend AI to self-destruct a sector) High danger
Abductors (Advanced aliens seeking to abduct humans and perform weird experiments of them, then return them to cause chaos) Low danger
Culti of Nar'Sie, the geometer of blood (Cultists using power of banished god, trying to summon it back to our world) High danger.
QUICKEDIT: Okay, this took WAY longer than I anticipated to write.
