The Vault appears on the surface to be quite a conventional prison, run on quite enlightened grounds. Prisoners are expected to find good use for their time, in exercise, work or study; suitably qualified inmates can also teach. There is ubiquitous surveillance, but that isn't too surprising in a prison. The Vault is made up of a number of Annexes, distributed around in geographically separate locations, which are all tied together so with a bit of admin work prisoners can interact.
If fact, this is all a virtual environment, running at just about real world quality. The bodies of the inmates are in a protective and regenerative suspended animation state, and their minds are stimulated to a conscious state, though running a bit slower than real time. The staff are AIs, running multiple instances, each with individual characters. Except the Warden, who runs the place. The underlying system is based on an ancestor of the "Metaverse" virtual world.
Non-AIs can be hooked-up to the system, to visit or interact with the inmates; teaching might be done this way. Some inmates may work in gardens, or on (simulated) external projects. If needed, inmates may be released, though all undergo a "medical examination" on leaving, where they are awoken back to real life. The process on entering The Vault isn't dissimilar. The various parts of The Vault, the Annexes, are tied together by a net of FTL communicators (the 'very difficult to find the end-points' variety).
Quite major efforts are made to ensure that inmates benefit from their confinement. The aim is that they leave at least as healthy as they arrived. And, no longer criminals. While physical activity may not give full benefit, research shows rehearsal of activities does improve them. Mental activity will have much clearer long-term effects.
The Vault was first built in Kandor City, after it became clear that the first design for a Supers prison, the 'Phantom Zone Projector' project, just wasn't acceptable. The Annexes are multiple underground structures, each of which consists of 'perpetual' power supplies, a redundant array of waved server farms, which runs at least one AI and the simulation, and the actual inmate confinement area (ICA). The ICA has its own triplet of 'perpetual' power supplies and primary and backup suspension units, with dedicated medical support units.
Few annexes have more than a couple of dozen prisoners, though they are all rated for fifty. The annexes are heavily shielded, and are rated Moon-quake proof; on Earth they'd be considered pretty good nuclear shelters.
Access to the annexes is via KAR (Kandor Automatic Railway), and every so often, 'for administrative reasons' (also personal interaction problems), prisoners are moved between annexes (in their sleep). Inter-annex communication is pretty good (holo conferencing might be allowed), so this shouldn't cause too many social problems. The recycling is pretty good, but if needed KAR also delivers all needed supplies. Prisoner release is done via KAR to one of several Kandor City official buildings, after a 'medical examination'.
Prisoners are placed in an annex via KAR. A number of carefully annonymised transports, five to eight in number, are sent out in quick succession, and only one contains the prisoner. All the transports will be automatically cleaned before further use.
Note that The Vault also holds criminal AIs, and it is made quite clear to these they will be operating in a highly constrained environment, and regular backups will be taken of them. Their privacy will not be intruded on, but if things go wrong they may find themselves 'running' a previous version of themselves.
A variety of drones are provided for AIs to interact with other prisoners, and if they are resident in a fixed body, that's what they'll believe themselves to be using (maybe with some hard-wired constraints to prevent escape). If they didn't sleep before, they'll find they've acquired that ability, and need.
Prisoners with really unconventional metabolisms, say due to a biomod, will end up in one or more specialised annexes that have customised facilities. They may be suspicious that they acquire the ability and need for regular sleep while they're in The Vault - but this may be good for their long-term mental health.
The Vault looks like a holo-enhanced immense underground cavern, with an artificial day and night cycle, to the prisoners. There are a number of other structures visible some ways off, but it isn't clear if these are real or fake, due to the 'holo haze'. Over time, it will become clear some of these are other Annexes. Presumably some are guard buildings.
Hazy figures and non-human shapes can been seen moving between the structures when the light is right - these can be assumed to be concealed guards and guard-bots. People sometimes come and go via light electric buggies. When people move between Annexes, or enter and leave The Vault, they drive for a while through a holo fog, taking a number of turns, at forks and cross-roads on their path. Prisoners are moved between Annexes while asleep, and other prisoners don't get to see them come or go.
There are about fifty people, AI and not, who know this is a simulation. Some were on the design team, that was given the 'underground cavern' specification and told to make it secure, some on the (anonymous) ethics over-watch group, some on the actual running staff. Yes, they know that sooner or later the secret will get out - some are amazed it's lasted this long.
Dr. Asmodeus Grey was on the design team. But, he hasn't told anyone else. He considers it amusing, and is keeping the knowledge as a 'card', in case he needs it. (He's worked-out how to become a prisoner, and leave when he wants to, for example.) In fact, he killed a number of criminals who found out, and he didn't think would be closed-mouthed enough about it.