I’ll try and keep things brief and to the point. If all your looking for is a pointer on reaching a Skully on any given floor then I suggest using the index. The rest of this section covers some basics on what to do to find Skully locations without explicit details on any given location.

First off if you are trying to find everything on each floor before you move on to the next, you can't get to any of them without the equipment you will find on later floors. You can't get access to any of the Skully locations without at least Turbo-Motion Boots v2, and I would recommend waiting until you have Turbo-Motion Boots v3 before you go back to previous floors to hunt down Skully locations. As far as I know the earliest you can find the v3 boots in on Floor 7 Systems Engineering.

The hiding spots on the Reactor, Medical, and Research Labs floors are only reachable with the v3 boots outside of someone finding a glitch or gets lucky and a wall section lets you rest on it without falling back to the ground. All of the Skully locations are in high up nooks that are unreachable without the additional boost from v2 or v3 boots. You get this boost by jumping and holding the jump button. For v2 boots you will get a brief moment of upward trust and the v3 boots give a significantly longer period of upward thrust when the jump button is held down.

If you are using the v2 boots to reach hiding spots, I can almost guarantee that you will need to hug a wall and hope you can find a section of the wall that lets you rest on it without having to fall all the way back down to the floor. This is part of the reason I suggest waiting for v3 boots as they will make the hiding spots significantly easier to reach.

Starting from the elevator to the reactor.
Take a left and head down the hall.
At the end of the hall take a right and go through the door.
Turn left, pass by the Radiation Shield Controls room on your left, and walk down the hall.
Take a right and walk to the end of the hall
Go to the left, head down the ramp, and turn right
Walk forward a bit and look to your left.
Look up
Yep it's up there
Hello Skully
Lets look at the map. Western side of the map

Starting at the elevator to Medical. Take a left and head up the ramp.
Take the first door on the left up another ramp.
Pass by the 'HERE' graffiti, and go through the 2nd door on the left.
Head through the next door straight ahead (may need to unlock it with the switch on the left wall).
There should be a ramp down that turns to the left.
At the bottom of the ramp walk forward and start looking up.
After walking a short distance you can turn around and see the ledge Skully is hiding on.
Take a running jump off the prev ramp and with the help of v3 Turbo-Booster Boots you can get enough vertical distance to greet Skully personally.
And now for the map. North Western corner in maintenance tunnels.

Lets start at the elevator in the Research Labs that is close to the Computer Room.
Take a left and head to the end of the hall.
Head through the door on the left with the radioactive warning signs.
There is one more door that leads into the Gamma Quadrant's radioactive trench. If you have not hacked the cyberspace terminal to turn off the radioactivity then make sure to head trough the next door straight ahead and turn off the rads or deal with the resulting rads you will be dosed with in the room as you go to greet Skully.
To the right of the door straight ahead is the spot we are looking for.
As you look up the entrance will become more obvious.
Another angle showing the ledge above that Skully is hiding on.
Get on top of this ledge.
Use the v3 boots to get up to the next ledge.
And a wild Skully appears.
Map Time. In the South Western corner of the map in the room leading to the isotope for shielding.

Note: the first time you are here the Maintenance tunnels are locked off. Until you reach a part of the story that requires you to head into the guts of Maintenance on a repair job this Skully will be completely inaccessible. If you turn off story this may be accessible all the time, but I have not tested this personally.

Starting from the large elevator in the center of Maintenance near the recycling station. Take a left and head through the door heading South.
The next door to enter is a little to the left. Keep heading South.
Now it is time to enter Gamma Maintenance.
Once through the door head to the right.
Walk all the way to the end of the hall.
Look up and the ledge will come into view.
Dr Skully I presume?
Gimmie that map. South Western corner in Gamma Maintenance.

Starting from the Storage elevator go forward a little look to the right.
Head down the ramp leading to the Recycle Station.
At the Recycle Station look to the right at a stack of crates.
Above those crates is a vent leaking bloo.. I mean strawberry jam.
Skully has been extra hungry since being stuck in the vent up here
More maps. Near the center of the map not far from the elevator.

If your starting at the Elevator from Executive, turn right and head down the hall until you reach a door.
---------------Alternatively---------------
If your starting at the large elevator from Maintenance/Storage then make your way to the northern section of the map and look for the fancy Executive carpeting as shown in the screenshot.
Take a left and go through the door. If your coming from the Executive elevator this is the door previously mentioned.
This is the Desk at the entrance of Flight Bay 1.
To the right of the door is a ramp leading up into the hanger for Flight Bay 1.
Inside is the shuttle that you will need to boost jump on top of.
Once on top of the shuttle look for a gap in the railing to make getting on top of the upper catwalk easier.
From there head to the eastern side of the upper hanger
There should be a bulkhead that can be opened. If you find one that can't be opened, then you are on the wrong side of the hangar and need to head to the opposite side.
Skully prepped and ready for takeoff.
Even more maps. Northern end of the map in Flight Bay 1.

Head to the entrance to the Beta quadrant that houses executive suites, and ultimately leads to Diego's living quarters.
Once through the door leading to Beta there should be an energy station to the right.
To the left is a long hallway that you need to head down till you reach the first set to doors to your left and right
Head trough the door on your left (going North).
The bookcase directly North of the door is close to where Skully is hiding.
If you look up and to the left the ledge should become more obvious.
Skully at the ready in their safety crate.
Maps below. In the Southern section of the map, but not at the outer fringes.

From the elevator from Executive go forward and take a left.
Head down the ramp and turn left.
Go down another set of ramps and go over/around the crates.
Head through the door and enter the Core of Systems Engineering.
Approach the pillar to the right, in the center of the Core room.
As you may have guessed Skully is hiding in ceiling of this room, and it's a long way up.
The hiding place is located in the southern part of the Core. Way up there.
The ladder nearby can be used to get up to the next floor.
But the rest of the way will require jumps using the v3 boots.
After the first jump it's time to get on top of the metal beam next.
And for the last jump you'll need to jump up around the beam above your head and get back on it.
Skully is putting your new v3 boots through it's paces now.
Maps for the lost or curious.

This Skully is near the top of the central spire in security. I am going to show how to get it after the holo bridges are activated and the central ladder is accessible, but you will need to progress through the level normally first to activate these bridges. Also be aware it is possible to reach the top balcony with some careful booster jumps without having to use the holo bridges, but since that is difficult to show in screenshot form I focus on the intended path. After the maps I will use a few pictures to show how to get up there without using the force bridges.

Starting from the entrance into Security from the elevator to Systems Engineering. look for the holo bridge on the left.
Use the grav lift to get up to the holo bridge.
Disable the electric mines on both sides of the bridge, cross it, and go through the door. If the door is still locked make sure holo bridges are active and that security has been lowered.
Once you reach the center of the shaft a long ladder in a irradiated room awaits you. Activate your Enviornmental Protection Pack, or pop meds to deal with the damage as you climb.
Once at the top a single door awaits
Then another holo bridge with mines that need to be disabled before crossing.
Once across, don't go through the door on the other side and instead turn around to look for a ledge to the left across the gap.
After you take the jump this is the view of the bridge you jumped from.
Open the door on the ledge you jumped to and Skully will be in sight.

Look at you mapper. The ledge you want to reach is high up on the North Eastern corner of the central spire in Security.

Alternate path
On the bottom of Securiity look for the Extraction area to the North of the central spire.
Keep heading up grav lifts and you should reach Monitoring.
After one more grav lift you should arrive at this ledge and holo bridge area.
From the ledge you can jump to this alcove
From the alcove you can jump to the large structural beam shown on the left
Once there you can probably jump to where the holo bridge is shown in the picture, but there is a small ledge that will get you closer to the desired ledge so I suggest jumping there first.
Now the final big leap will get you on the final ledge.
And from there it's the last leap to victory same as the other directions have shown.

Starting at the elevator from Security take a right and head West.
Keep heading West, and after going down and up some ramps you will arrive at a large room. Head across the room going South West.
You should find two doors. Enter the one that is brightly lit.
After heading North for a short distance you should find the armory door. Head inside.
At the bottom of the ramp there should be strawberry jam running down the wall to the right
Skully's been busy snacking up there. Let's come up and say hello.
Skully made quite the mess up here.

A pathetic pile of lines and charts. The final location is on the North Western fringe of the Bridge.

Thank you Nightdive Studios for getting this out in great shape. Wish the road had been a little less rocky along the way, but sometimes the best intentions don't pan out. You stuck with it and got it done. Now more people can experience this absolutely fantastic classic without having to fight a control scheme that took too much inspiration from simplified submarine sim controls and a UI that did not age well. Almost all the modernization changes and adjustments do a fantastic job of making this game significantly more playable while still being System Shock 1 at it's core.

If anyone wants to use the information here for a comprehensive guide feel free as long as you state where the info came from (a link would be a good idea), and don't just copy paste the info from my guide.