Point Prometheus

* Entry From Apollo_Square
* Connects to Proving_Grounds
* See also Big Daddy and Little_Sisters (made in this facility)
* See also Suchong
* See also Amended_Game_Level_Maps
Map orientation is taken from the Bathysphere coming from Apollo Square - from the South East ( or rather from Olympus Heights, which would have been the logical Bathysphere cableway 'hub' location ).
Note some parts of the levels below 0 can be seen detailed on the Proving Grounds level maps ( Bathysphere Station, etc ... )
Not Shown here : Levels below 0 ( partially seen on the Proving Grounds Level maps ) which include a Trolley Return Loop ( terminus of a trolley line coming from the South ). Parts of those deeper levels likely were retrofitted/ADDED when the city Trolley system was consolidated into Rapture Metro Transit, and the Trolley tracks/tunnel/viaduct were built to connect into this level's building complex ( excavated out of the bedrock underneath ).
Level 3 of this Map corresponds to Level 3 (main entry) of the Proving Grounds level maps (most of that building is lower than Point Prometheus as its build in a shallow seabed valley).
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==Fixes ==
I had to stretch the safety/Security Airlock passage link to Proving Grounds (on that map) quite a bit so that there is no overlap of the Proving Grounds building with this level's Bathysphere Station. Note that every Viaduct connection between buildings also acts as a Safety Airlock. They have Securis doors on each end interlocked so that if a pressure differential occurs the doors wont open, protecting adjacent structures from possibly disastrous flooding.
Since the Bathysphere Station has a window showing 'the sea' on the side up against the entryway to The Proving Grounds, I had to do 'the Aquarium fix' yet again ( that stretched hall now has a long "Living Fossils Aquarium" on the wall the Bathysphere window looks into ).
The Entranceway past the viaduct in from the entry Bathysphere Station likewise has been stretched a little to avoid overlapping parts of the Proving_Grounds map. There probably would have been something in this space - services for the Workers and visiting public ( from before it became a 'Big Daddy' factory - used for Diver Training and possibly Bathysphere maintenance ).
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Floating Rocks (seen out of windows) : I've filled in seabed to support those rocks ( on the level 0 below ) and with some graduated surface indications to show the bedrock the building Foundations rest in.
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Fix the Usual faked outside window-view issues :
* Issue : exactly the same cityscape scene is visible when looking out windows for all of the 4 cardinal directions ( the same Skybox view is reused ), and the caricature adjacent buildings having far too many windows, the distant buildings being WAY too tall, etc ...
* External walls that have no thickness per what a structure at the depth would need - corrected.
* A building wall seen through a sea window IS part of an accessible adjacent building of the level, but they show those building facades covered in windows, when the corresponding building interior either has no windows in evidence or none of that pattern.
* A common weirdness with outside big 'rocks' ( part of the sea floor apparently ) being there, while so many of the Skybox views make it look like we are a dozen stories above any seafloor. Best just to discount the tall 'grand view', as we are almost always (in the game) within squat horizontally sprawling buildings which have only a few floors/stories.
* Looking out from the Double-level viaduct ( leading to the Little Wonders facility ) has blocks of concrete visible to its sides attached to that building. Some of the interior spaces stick out past the position of Viaduct's (weak) sliding doors ( better if they were Securis doors to protect from flooding the whole complex ). My Construction has all the exterior wall thicknesses increased and made more monolithic, so I've solidified that wall and shortened the viaduct windows.
* The Failsafe Armored Escorts South Wing has West windows with a sea view of distant buildings, when the Mendel Family Library building section is almost immediately adjacent within that same space. That was fixed by keeping the window, except have it look into another Training Test Tank. The South windows with a similar long view are OK, except that they would look down onto/across the roof of the ( now added ) AE Train Station on the Proving Grounds level map.
* Optimized Eugenics - Several exterior walls/pillars are visible on one window, but are gone when same view is from an adjacent window ( window on other side of where the wall/pillar was seen ).
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The Test Tank adjacent to Failsafe Armored Escorts has 2 circular hatches to access the interior, but they were botched by being right up against a thin wall that would pass directly to the adjacent room/corridor (blank wall there). This was corrected by the section being stretched to allow for thickness of walls with passages within. This also resulted in making the entire building simpler ( more monolithic ). Complementary hatches were added to properly create airlocks ( as would actually be needed ).
Water passages now link to the larger 'pool' in the Suit Assembly area to make a much more extensive testing/training environment for all the maintenance activities the Big Daddies/Maintenance Cyborgs do. An airlock to the Ocean allows further Training in the external (Real) Sea Environment.
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Added - some of the Adjacent Building visible from Sea Windows ( actually represented by caricature facade models ). Some buildings are from what is visible in the Proving Grounds level map (and overlap into this map) and overlap. One view from the Southern end of Failsafe Armored Escorts ( Candidate Conversion ) is actually attached to the same building you are in, but is at a lower level ( so you still see a horizon view, but not the looking down onto the roof ).
The Sewer level here is below level 0 (so not shown) with the Metro Trolley (also below level 0) running above it in a viaduct. The Trolley line terminates at Point Prometheus, so it has a track 'loop' to efficiently turn the Trolley Cars for heading in the opposite direction ( The Trolley 'return' loop is also below level 0, so not shown on this map ). The loop runs in a tunnel constructed in the seabed ( which was much cheaper than the conventional 'viaduct' style structuring ). More than a little of the (1952-53) consolidated Metro Trolley system has tracks running thru tunnels, which lowered the additional construction costs significantly as well as straighter routes.
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The usual city utility lines ( Heat, Power, Water, Air, Pneumo, Communications, etc... ) connect Southwards. Redundant utility 'aqueducts' run SouthEast and East to other clusters, and also continue Northwards towards 'The Shallows' where farming/industrial businesses closer to the surface existed (in the MMORPG). The connections are with the sewers running on lower levels not seen in this map set ( see Olympus Heights maps for equivalence ). Level 2 has lots of utility spaces and access for various machinery, as well as the quite high ceilings of some sections of the floor layout below (where we walk).
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Added - a second Bathysphere station used by the Point Prometheus companies personnel ( those high enough grade to afford it ) to improve traffic flow which is pretty restricted by the original single load point/dock. The Bathysphere's Cableway mechanism is below the visible levels with the route running back towards the major hub at Olympus Heights ( both share the same expensive infrastructure cableway equipment ). Access stairs also links to lower level Staff facilities with Cafeteria and other needed functions (like restrooms). There would be a 'Transfer' Bathysphere Station linked to the adjacent buildings Northward, as there are no connecting viaducts into the central buildings on this map.
Added - a AE Station Mk2 and Trolley Station to be shared with Proving Grounds ( previously Rapture Museum ) in an overlapping transit hub which ties all the different transportation system together. Details will be on that map. A building visible while in the Proving Grounds level was selected for this and added on this map because it was in the right place to be part of a shared transportation hub between 3 different map sets ( Point Prometheus, Proving Grounds+DLC Museum, and 'Fontaine' -- all are in close proximity ). The East entryway of the Atrium now instead of being a dead end, leads to the added Trolley Station.
Added - a Jet Postal Pneumo mail station. No doubt many small shipments were shuttled to the facilities in this complex from other locations in Rapture ( like Ryan Laboratories and Fontaine Futuristics ). The amount of paperwork involved in the projects likely were significant.
Added - the usual lower level sump drainage passages ( basement areas are largely filled with filler concrete to anchor the buildings, with utility access/sump tunnels thru them ).
Seabed is shown (from visible hints) in places, while others are probably lower than level 0 ( but not being that ridiculous height seen in those odd Skybox external views ).
Point Prometheus was a City Cluster ( or at least the building we are in ) developed/redeveloped by Fontaine as a Technical facility for ADAM tech and 'harveter' Little Sisters, and later for producing 'protector' Big Daddies ( likely developed and existed much earlier as City's Maintenance Cyborgs ). 
We elsewhere saw had seen Orphanages, which were a source of the raw ADAM materials ( there must've been ALOT of Little Sisters, compared to only the few we ran into. There were even MORE Big Daddies, as there also should have existed a large labor force for maintenance, BESIDES the ones being 'Protectors' ). In the MMORPG, we should see remnants/documentation of the Atlas period ( and earlier ) protests against the 'Big Daddies' as diver maintenance workers stealing jobs from human workers ... 
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The Firing Tunnel in the Suit Assembly line sticks way out from the rest of the general outline of the original building structure interiors. It is no longer a problem since I just extend that entire side to preserve the clean monolithic lines of the building's structural wall ( extra utility space can fill in the additional internal area that it creates. ) A similar clumsy 'sticking out' is in the "Autopsy" room in Little Wonders.
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There is a Huge amount of Utilities in this facility ( much in the overhead in the production area interiors ).
On other level maps, we've seen a number of "vents" we went thru as a sneak path, or as a way past some obstacle in the game. Most of these building have far more such accessways which are not represented on these maps. There would be access hatches to various utilities, manhole covers to drainage channels, and lots of ventilation ducts ( made large enough to be entered and cleaned easily ). The building spaces all are partitioned into airtight sections to isolate potential major leaks, and they have airlock hatches to allow passage thru the partitioning. There are many subfloors and false ceilings and false walls offset from the thick concrete structural walls ( which all slowly leak or precipitate moisture due to the oceans coldness, and have to be systematically drained ).
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==Observations==
What was of Point Prometheus before ADAM existed in Rapture ? Was it a later added/added-to cluster ? It is adjacent to a Museum that probably was part of the originally city plan, and it is near that tall building "Prometheus Point" ( where Fontaine's lair was ). We never saw what all was inside most of that large building. Diver Maintenance training would however have long predated the 'Protectors' ( and even the name "Big Daddy" ).
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Mendel Family Library : An example of extensive amounts of possessions brought to Rapture by various immigrants, and additional research materials for various enterprises brought in from The Surface. NEWER technical research materials would be brought in from the Surface ( possibly quite alot even after the 1951 contact ban using official channels to preserve Rapture's secrecy ).
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This Entire Complex had been taken over by the City Council after Fontaine's demise, and the Big Daddy program had been added to the existing Maintenance Cyborg program ( which predated the Little Sister stuff by several years - the purely Maintenance units may have been less heavy (less armored) to facilitate their work instead of being made into 'tanks' ).
On wonders why those previously existing Maintenance Cyborgs had not been used as weapons in the %27civil war%27. Perhaps they were just too unmaneuverable, but you would think that they at least could be used in defensive positions and could have had extra armor added. Perhaps any attempt to completely change their purpose would have taken too long to develop/modify, and the existing Cyborgs were difficult to change their conditioned from their original tasks ( ie- non-violent considering how strong they were, and that they were converted from criminally insane inmates ). Perhaps they were hard to control or when without a fixation on an object for their task they did not work so well ( Note- later use of base instinct in regards to Little Sister protection, somehow ... ).
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The reason the Tall building near Point_Prometheus (The 'Fontaine' level maps) can be the 'highest point in Rapture' ( besides some industrial and farm installations to the North of this area ) is because it is in the leeward (down current) shadow of the top of the SeaMount named Mt Ryan ( the extinct volcano Rapture is built on and which the Lighthouse is at the pinnacle of ) which prevents the infrequent passing iceberg from crushing/shearing off the top several hundred feet of any building close to the ocean's surface.
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The 'airlock' double-set sanitizing ( Decontamination/strylization ) doors leading to Optimized Eugenics and to Failsafe Armored Escorts do not actually interlock properly when a Security Flybot follows you through BOTH doors ( the red-green thing doesn't block them ).
Those airlocks also would have made a GREAT location for at least one Jump Scare ( early on, so you would be wary of them all the many other times you would go through doors ).
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Fiendish Things That Fontaine Did Seem To Have Gone On Here : 
The Dissecting of children ( that nice surgery/operating room with the autopsy type tables ) seems more from the early days when Fontaine and Tenenbaum did that kind of thing ( implanting Sea Slugs and such ). The conditioning processing of Little Sisters to accept BDs would be from the later time ( when Gathering was possible and later adding their Protectors ).
There seem to be alot of these in the Little Sister 'conditioning' section of Point Prometheus. Possibly it is implying that they 'went through' alot of children to produce the required number of Little Sisters ( or to develop a working system 'in the first place' ) . The large facility seem to have existed BEFORE Ryan took over Fontaine Futuristics on Fontaine's 'death'. So THAT could be the locations of the original Slug Implantation Process. 
A Little Sister would need to be a proven 'Producers' BEFORE being sent to be warehoused in the Orphanages - Those that weren't 'effective' might be disposed of - like the way milk cows are 'culled'. Efforts probably would be taken to preserve the SlugReally is odd how all this abuse of children on such a scale could be kept secret. Such abuse would NOT be tolerated, and Fontaine would be finished if it was found out. Convenient that Little Sisters get blamed on Ryan, No ?
OR this could be one place Fontaine's 'Slug Hosts' were held, and the ADAM 'extracted' from them ( Seems too small for the number needed for that process to to be just here - Perhaps that process was developed and R&D was done to IMPROVE that process ... )
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What exactly was this place BEFORE Big Daddies were being made - late in Rapture's history :
Removed Doors and Signs "Fontaine Futuristics Genetic Research Dept". Even before that - its a large building complex (Fontaine Futuristics was big enough, and adding this facility LATE in Rapture's building history - post-ADAM discovery/development would have been a major undertaking to be built NEW.)
Little Sister Department - OK, that predates 'Atlas' ( used for the research and implementation of Slug Implantations ) Its actually a Stand-Alone building (though the shape of the connected part of the main building looks to have been planned to have something connect to it). The facility would be only a step in the Process ( implantation and stabilization ), and most of the 'Symbiants' would be located elsewhere.
Creation of Maintenance Divers (Cyborgs) fits the other large parts of the facilities ( they were in BEFORE the Big Daddy 'Protector' had reason to exist ). Making Diver Dan 'cyborg' workers would have dated back at least as far as ADAM insanity (and genetic modifications) existed. Human divers before them ( for city Maintenance ) could have been trained in this facility, and probably divers may have got Dive Assisting Tonics (depth effects), and this place would be used for that research/development/application.
The BD training area has practice rigs for every activity the Maintenance Cyborgs did ( makes sense, no ? ), to allow Training for internal and external repairs and maintenance.
'Cy' the cyborg (aka "Diver Dans" as they are called by the Newsies). BTW - "cyborg" ( short for "cybernetic organism" ) is a being with both organic and Bio-Mechatronic body parts. The term was coined in 1960. The Rapture Novel mentions the word "Cyborg".
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"Marketing Gold" ( Audio Diary Analysis) :
Ryan : " I'll admit Fontaine showed some foresight when he built up the Plasmid business, but the man really never understood sales. Hiding those little girls beneath a bushel. I've just seen the preliminary design work on the new Plasmid machines, and they're exactly what I wanted. Mark my words -- presented properly, those Little Sisters are marketing gold."
It IS after Fontaine is 'killed', but is this before or after Kashmir ?? Likely before - at least talking about his plans to give some order to systematic distribution and restored ADAM production. Bootlegger's defective products no doubt caused ALOT of the ADAM-Disease problems ( Fontaine's product likely was as bad, as it WAS his goal to disrupt Rapture ). Remember, Ryan didn't want MORE crazies in Rapture.
Also regulated sales is very useful mechanism for (eventually) feeding Splicers the Pheromone 'Control' agents to get them under control ( and eliminating Atlas's influence of them ).
SO, its just 3 months to get the whole Fontaine Futuristic working ( after the Neptune's Bounty Shootout and before Kashmir ? ) All those facilities and employees and the ADAM production being restored/rebuilt/reorganized ?? It is very easy for ignorant game writers to make up such over-optimistic/unrealistic implementation of such complex tasks in their simplistic fiction.
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There are what appears to be Electron Microscopes in Eugenics Analysis. Its not only DNA that you are concerned with, but they are far more useful analyzing/monitoring the various BD modified tissues ( after all, THAT is what the DNA mods are all about achieving ).
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The Little Sister 'Conditioning' seems a bit minimal. I would at least add TVs in every 'cell' for a continuous conditioning process ( while various drugs are used to make them more susceptible to their required conditioning. ) Initially this was simply 'Pacification' of the child to control them while the Sea Slug did its work. Later the interactions with the Big Daddies would be FAR MORE complicated.
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The pre-Big Daddy use of this facility could be for Maintenance Cyborgs made from 'insanes' and possibly volunteers. ( The Novel actually mentions the word "Cyborg". ) It seems rather unlikely for 'civil war' emergency-driven Rapture to allow a facility this big to be suddenly organized/built ( or made subsequently for the 'Protectors' project ).
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Those big yellow vats are probably 'culturing' medium for the 'test subjects', which by the Game's time would be getting Big Daddy conversions. There are alot of genetic modifications which allow the Big Daddy to withstand sudden massive pressure changes ( so as to not get 'the Bends' when transitioning outside-to-inside the sea ), as well as having a great deal of Strength added to be able to move/work in those VERY heavy diving suits, and to operate the required tools. That is ALOT of tissue modification and additions - which don't just appear out of nowhere like magic.
They kinda skipped over that aspect for Jack's "conversion". He might not have to go into the ocean, but that suit weighs a great deal ( even without the tanks ), and is quite cumbersome. Jack shoulda at least got a battery of Tonics applied to him ( that step to be shown as part of the BS1 game ) as part of his pseudo-conversion.
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The BD facility does seem to take up alot of space ( even more is hidden in the utility spaces above and below the main floors ). For a facility this large, you'd think there would be a large number of Big Daddies in Rapture ( this place would double as the primary BD maintenance facility as well ). Its later existence depended on the Genetic/Physiological Modifications which ADAM made possible, and thus couldn't predate that -- except possibly as a Diver Training School used to supply the ordinary men who had to do Rapture's external maintenance before the Big Daddies were available. Those human divers BTW would be wearing Hardsuits. 
The later 'Splicer' divers may have been some of the earliest large-scale ADAM]] users, which may have precipitated insanity and conversion to more 'controlled' Maintenance Cyborgs who could then be joined by 'reformed' Insane Criminals ( who increased as ADAM use became more common ) also being converted to "Maintenance Cyborgs".
The name "Armed Escorts" was a bit misleading, as it was added quite late in the facilities existence. The Protector role being added to the previous Maintenance role - Post-discovery-of-ADAM. Big/heavy Diving Hard Suits require extreme strength to walk in, something which is unlikely without ADAM Brute strengths upgrades. 
Consider that 'rich' citizens might want their OWN 'Armed Escorts' - Something like the heavily armored Big Daddies ( and they could afford them ... It is something to add to the MMORPG ). Less bulky/more stylish models would likely be desired ( 1950s Fins !! ). Somewhat clumsy/ungainly to have in many social situations ...
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The Facility's (building) Foundation areas ( the sections largely filled with ballast concrete ) are not laid out too systematically, as the shapes of the buildings above were not themselves very regular. There are Access Ways within the mass of 'filler' concrete ( alot of that volume was embedded with large chunks of rock to provide solid mass rather than strength ). That Access was mostly to provide drainage for the inevitable seepage, and monitoring of pressure integrity.
Submarine style manual doors ( no need for fancy/expensive automatic doors down there ) were used to partition the space into many sections, to contain any major leakage long before it could be repaired. Utility areas and such are mixed in as well. Non-mapped ( deeper) levels often extended quite further down, and would show anchor piers driven/dug into the ocean bedrock. Utility and Sewer passages would be in those unshown levels. Big daddies who likely did alot of the maintenance would be instilled with OCD-like anxiety about "ALWAYS CLOSING THE F*CKING PRESSSURE DOORS".
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Shows that Fontaine constructed the place before Ryan/Rapture-Council controlled that Company. The Little Sister facility also likely was there BEFORE it was later used Post-Fontaine for 'Gattherer' training. The Maintenace Cyborg production there also likely predated 'Protectors' existing -- Sometime after the ADAM generic manipulation was developed in the early 1950s ( probably something similar to the 'Handyman' - of disabled men getting a new chance/purpose ).
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A gang ( normally each has only one ADAM-Extractor ) of Little Sisters seems to have stabbed this Splicer. Perhaps it was already dead ? Practice makes perfect. What would a group of Little Sisters be called ( ie- A 'Murder' of Crow, a 'Pride' of Lions, etc ... A 'Giggle' Of Little Sisters ? A 'Troop' ? The MMORPG should perhaps have a contest. )
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==Oddities==
That Voice Box shredding machine - Well Jack never says anything anyway, so what's the difference. They really should have (in the game) had to have Jack go get some Brute Strength (equivalent) Tonics to be able to operate in the Big Daddy suit ( which is supposed to be heavy enough to have neutral buoyancy in sea water -- 600+ lb ... ). But then those game developers couldn't really think of everything, no matter how obvious a detail/idea/opportunity.
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The Broken windows into the Decontamination 'Airlock' passages - when there are plenty of interior windows we cannot break, but these ones you would think would be quite well reinforced for security reasons ... But THEY are busted. Plot (writers) says 'Cuz'.
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"The Mendel Family Library" has alot of very weird diagonal angles in it, when most libraries rely on perpendiculars for their basic layout. Other than a bored level designer, I cannot see any reason for it.
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As usual, there are unneeded floor level shifts (steps) which should never exist in real life - because of the difficulties they impose of moving about equipment ( particularly in the 'manufacturing' areas of this level ). They were added by the level developers simply to give a little more variation to the floors, and in a few places to contain a puddle of leaking water from apparently flooding the entire level to that depth.
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Audio_Diary_Analysis - "Missing Boots" :
Dr Suchong : "Goddammit! The Big Daddy boots need to be shipped here, not to damn library! What kind of idiots is Ryan hiring nowadays ? This kind of bullshit never happen under Fontaine."
This is "Big Daddy" Protector - started after the Kashmir Massacre happened and the ADAM supply was impacted. Suchong is complaining, but it is possible that "Its Hard To Get Good Help These Days" may be significantly true. It is also a mechanism-oriented project not just testtube/lab science.
It was also a NEW and rushed project - not quite the same as the Fontaine Futuristics ADAM projects which had alot more time (and unknown schedules as new discoveries were made).
BD Shoes dumped into the Library ? Perhaps the person delivering the Boots got distracted by a Fine Book there, and then got hungry and went off to the Employee Cafeteria downstairs and totally forgot about the delivery.
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The Training Test Pools for Big Daddies - If something goes wrong, what exactly do you do to rescue them ? ( Have Hardsuit for 'staff' kept ready when Training is in Progress ). One hopes initial 'interior' 'in-water' testing would be in some kind of 'fast drain' type pool where the water can be vacated in moments ( like that small "Test Tank" ). Those indoor pools would have served for preliminary test/training (checkout of the 'Trainees' working their environmental systems).
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Little Wonders Educational Facility does not have a very large number of 'cells' to hold Little Sisters, and has that sinister 'Autopsy' section -- which is big enough for the morgue of a small city. The place looks more like a development site rather than the main LS 'production' facility. The conditioning section also is rather meager. Of course, later we see the much larger facilities at Persephone and more Orphanages in BS2. No Little Sisters are present, so what does that say about Ryan supposedly still running these operations - maybe by this time ( with Atlas virtually beaten ) Ryan is seriously working on how to eliminate ADAM from his City.
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There is also the Point Prometheus Multiplayer map - The same concept warped into the circular MP map form:
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Point Prometheus Facility/Complex Questions :
The game writers wanted Ryan to be 'the bad guy', so of course emphasize the whole 'Turn children into Lil Monsters' thing, but Fontaine had to have multitudes of LS being 'milked' for ADAM (long before Ryan 'seized' Fontaine Futuristics) to support his extensive ADAM product production. So it is quite likely most Little Sisters preexisted Ryan's running Rapture's ADAM industry. The 'child' snatching incidents ( which we get anecdotal evidence of ) is not too clear about how prevalent that was, or when, or by whom. We dont know how many Little Sisters predated Fontaine's 'faked death', or even if there was also widespread activity of ADAM Bootleggers, who needed their own child slug hosts.
We see Point Prometheus sometime (a year or more) AFTER the so-called 'civil war' started, and the Gatherer/Protector programs were put in fulls wing ( AND WHEN unclaimed bodies are plentiful justifying it ). Earlier, there may have been some "Gathering" from living Splicers -- Perhaps it may have been done while investigated as a method to control incarcerated criminally insane Splicers ( to get as much of that dangerous special-ability-enabling ADAM out of their bodies ).
Why does Atlas/Fontaine run to Point Prometheus, IF he did not have 'a hand in' setting up the BD facility originally ?? Likely it is one of his abandoned/seized facilities, and the way to his Lair ...
The 'armored escorts' (Protectors) would be a logical successor to the pre-Big Daddy 'maintenance worker' programs ( and make use of similar/same facilities ). We dont know if the Alphas were built there also.
The Big Daddy building/making facilities are substantial, and really don't look like the quick product of a war emergency situation ( would not need the 'happy' signs ... The building looks purpose built ... The Maintenance Cyborgs made from criminally insane Splicers ( and other disabled people similar to the Handymen ) could predate all that 'Protector' thing by many years.
Suchong worked there while the Protectors ( ignore that broken BaSzx addon Retro-Canon that he died alot earlier ) were being created/perfected/produced. Some similar work may have been done for the City's Maintenance Cyborgs ( years earlier ) with all the genetic modifications they would require.
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The Education Facilities for conversion processing/conditioning the 'host' Little Sisters ( pre-Gathering ) might preexist there ( maybe Fontaine referred to them as his "Golden Goosies" ? ). The 'cell' complex is a seperate building linked by a Viaduct, and may have been added on to the complex or modified. We see proof that Little Sisters WERE conditioned/trained there ( BS1 ... the whole Persephone complex was a game in the future ).
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That Adjacent Museum complex converted into a Gatherer/Protector training area does look quite expeditious ( and Ryan may have been considering using 'Armed' BDs as 'soldiers' - If the 'civil war' went on for much longer ).
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It is a bit odd that Fontaine would still have that huge setup at the top of that large adjacent building without Ryan knowing/having it seized/dismantled/sealed-up. Fontaine supposedly never Spliced, so how likely is it to have that whole mechanim there to desperately overfill himself with ADAM ??? ( Which he would have known would be eventually fatal ), when a really good escape submarine to take him quickly to The Surface World ( and the Greater Fortunes/Power ) -- which WOULD have been a MUCH better/logical contingency ???? 
Unfortunately, The BioShock Game Plots are not "great" literature, AND often illogical ...
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Daddy is Dead and the Little Sister is unprotected.
WHAT WILL YOU DO ??
Of course, there WAS a THIRD option : of NOT killing the Innocent Big Daddy - Who's death did not seem to matter in the game designer's "Good Ending/Bad Ending Calculations.
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