I walk into the room with her and I can roam all over it, search her, pick up her gun, leave, come back, and nothing happens. The reveal never happens, deck 4 remains locked except for the one door to that room and I can't progress.

Anyone have an experience like this and is there a way to force it to trigger? I don't split saves like a madman so I would essentially have to restart the game if I can't figure it out.

as long as you have the autosave, the situation should be salvageable, no matter what has happened.

anyway, this has been an issue with some older (DE) builds, so make sure you are up to date - check SS2 community fixes.txt, the last few lines should read "updated core files to 2.48". once you are up to date, loading the autosave and running to trigger the scene should work. also, NOT having the game in program files is a good idea, as always.

post your ss2.log if that doesn't help.

I am on 2.48 which I assume was done automatically since I installed it through GOG Galaxy (I initially got the game when it was free for installing the client).

I don't have the autosave because I ran around assuming I had just missed something for about an hour before suspecting that it was a bug considering my run through Hydroponics saw me about 95% done with the area before I realized I was supposed to pick up and research the canisters.

Recalling anything weird that might have happened, the best I could think of is that after loading in from the bulkhead loading zone the door to the hallway looked like it was already open and had just finished closing when I was done loading, so maybe that messed up the trigger? Although this has been a pretty consistent behavior with the doors and loading zones everywhere else.

Here is the log.
---------------------------------

: PID: 4452
: CPU: arch=x86-64 , fam=586 , cpus=8
: SIMD: SSE=3 , 3DNow=0 , MMX=1
: OS Version: 6.2.9200
: Desktop resolution: 2560 x 1440
: Virtual desktop resolution: 4480 x 1440
: -----------------------------------------------------------
: Command line: "C:\GOG Games\System Shock 2\SS2.exe"
: -----------------------------------------------------------
: CWD: C:\GOG Games\System Shock 2
: -----------------------------------------------------------
: App Version: System Shock 2 Patch Final 2.48
: --------------------- misc config -------------------------
: resname_base .\+.\Data+.\Data\res
: cd_path .\
: load_path .\+.\misdml+.\Data
: script_module_path .\+.\Data
: movie_path .\cutscenes+.\Data\cutscenes
: mod_path patch_ext
: uber_mod_path osm+ubermod
: install_path .\
: language english
: game_screen_size 2560 1440
: game_screen_depth 32
: game_screen_flags 45
: game_full_screen 1
: screen_size 640,480
: screen_depth 16
: d3d_driver_index 0
: game_hardware 1
: single_display_mode 2
: ui_scale_mode 2
: use_d3d_display
: d3d_disp_scaled_2d_overlay 64
: framerate_cap 100.0
: SlowFrame 4
: SlowFrameUI 10
: force_32bit
: force_32bit_textures
: mipmap_mode 2
: lm_mipmap_mode 0
: lm_init_texmem 2
: lm_filter_margin 1
: tex_edge_padding 2
: alpha_test_as_opaque
: d3d_disp_enable_atoc 1
: multisampletype 8
: d3d_disp_enable_distortionfx
: sfx_device 1
: sfx_channels 24
: sfx_vol_music -1777
: sfx_vol_2d 0
: sfx_vol_3d 0
: sfx_mixer_timeout 200
: game shock
: obj_min -6144
: obj_max 2560
: max_refs 10240
: gui_font fonts\mainfont
: skip_intro
: crop_movies
: new_mantle
: z_far 512
: render_weapon_particles
: legacy_force_match_unrefs 0
: shock_single_bind_set
: shock_quicksave_slot 13
: shock_autosave_slot 14
: edit_screen_depth 16
: -----------------------------------------------------------
: Enumerating D3D9 adapters (2)...
: Adapter 0
: device name: \\.\DISPLAY1
: driver : nvldumd.dll
: descr : NVIDIA GeForce GTX 980 Ti
: driver ver : 0x001B0015-000E1456
: vendor id : 0x000010DE
: device id : 0x000017C8
: subsys id : 0x2B62103C
: device guid: D7B71E3E-5488-11CF-DA67-6C0B1BC2
: desktop res: 2560 x 1440
: Modes
: 640 x 480 x 32
: 720 x 480 x 32
: 720 x 576 x 32
: 800 x 600 x 32
: 1024 x 768 x 32
: 1152 x 864 x 32
: unsupported mode 1176 x 664 x 32 (not in mode table)
: unsupported mode 1176 x 664 x 32 (not in mode table)
: unsupported mode 1176 x 664 x 32 (not in mode table)
: 1280 x 720 x 32
: 1280 x 768 x 32
: 1280 x 800 x 32
: 1280 x 960 x 32
: 1280 x 1024 x 32
: 1360 x 768 x 32
: 1366 x 768 x 32
: 1440 x 900 x 32
: 1600 x 900 x 32
: 1600 x 1200 x 32
: 1680 x 1050 x 32
: unsupported mode 1768 x 992 x 32 (not in mode table)
: unsupported mode 1768 x 992 x 32 (not in mode table)
: unsupported mode 1768 x 992 x 32 (not in mode table)
: unsupported mode 1768 x 992 x 32 (not in mode table)
: unsupported mode 1768 x 992 x 32 (not in mode table)
: 1920 x 1080 x 32
: 1920 x 1200 x 32
: 1920 x 1440 x 32
: 2560 x 1440 x 32
: 1400 x 1050 x 32
: Device Validation
: validated ok, device added (0, E390000)
: Adapter 1
: device name: \\.\DISPLAY2
: driver : nvldumd.dll
: descr : NVIDIA GeForce GTX 980 Ti
: driver ver : 0x001B0015-000E1456
: vendor id : 0x000010DE
: device id : 0x000017C8
: subsys id : 0x2B62103C
: device guid: D7B71E3E-5488-11CF-DA67-6C0B1BC2
: desktop res: 1920 x 1080
: Modes
: 1920 x 1080 x 32
: 640 x 480 x 32
: 720 x 480 x 32
: 720 x 576 x 32
: 800 x 600 x 32
: 1024 x 768 x 32
: 1152 x 864 x 32
: unsupported mode 1176 x 664 x 32 (not in mode table)
: unsupported mode 1176 x 664 x 32 (not in mode table)
: unsupported mode 1176 x 664 x 32 (not in mode table)
: 1280 x 720 x 32
: 1280 x 768 x 32
: 1280 x 800 x 32
: 1280 x 960 x 32
: 1280 x 1024 x 32
: 1360 x 768 x 32
: 1366 x 768 x 32
: 1440 x 900 x 32
: 1600 x 900 x 32
: 1680 x 1050 x 32
: unsupported mode 1768 x 992 x 32 (not in mode table)
: unsupported mode 1768 x 992 x 32 (not in mode table)
: unsupported mode 1768 x 992 x 32 (not in mode table)
: 1400 x 1050 x 32
: Device Validation
: validated ok, device added (1, E390000)
: Enumeration done
: D3DProvider: Enumerating adapter 0 modes
: 640 x 480 x 32
: 720 x 480 x 32
: 720 x 576 x 32
: 800 x 600 x 32
: 1024 x 768 x 32
: 1152 x 864 x 32
: unsupported mode 1176 x 664 x 32 (not in mode table)
: unsupported mode 1176 x 664 x 32 (not in mode table)
: unsupported mode 1176 x 664 x 32 (not in mode table)
: 1280 x 720 x 32
: 1280 x 768 x 32
: 1280 x 800 x 32
: 1280 x 960 x 32
: 1280 x 1024 x 32
: 1360 x 768 x 32
: 1366 x 768 x 32
: 1440 x 900 x 32
: 1600 x 900 x 32
: 1600 x 1200 x 32
: 1680 x 1050 x 32
: unsupported mode 1768 x 992 x 32 (not in mode table)
: unsupported mode 1768 x 992 x 32 (not in mode table)
: unsupported mode 1768 x 992 x 32 (not in mode table)
: unsupported mode 1768 x 992 x 32 (not in mode table)
: unsupported mode 1768 x 992 x 32 (not in mode table)
: 1920 x 1080 x 32
: 1920 x 1200 x 32
: 1920 x 1440 x 32
: 2560 x 1440 x 32
: 1400 x 1050 x 32
: D3DProvider: Enumeration done
: sw framerate cap requested (10000 us)
: D3DProvider StartMode: smode 2560x1440x32 ; mode 640x480x32 (5 9 0 2D) ; 2d_surf_mode: 0
: CreateDevice: res = D3D_OK ; 2560x1440 fmt=22 zfmt=75 cnt=1 ms=8 swap=1 fs=1 hz=0 pres=1 flags=2
: Loaded script module "allobjs.osm" [FileModDate=2020-Sep-06]
: Failed to load script module "cutscene.osm" (error code 126)
: Loaded script module "Squirrel.osm" [FileVer=1.0.2.0 ; ProductVer=1.0.2.0 ; FileModDate=2020-Sep-06]
: sw framerate cap requested (10000 us)
: D3DProvider StartMode: smode 2560x1440x32 ; mode 1280x720x32 (7 9 1 3D) ; 2d_surf_mode: 3
: sw framerate cap requested (10000 us)
: D3DProvider StartMode: smode 2560x1440x32 ; mode 640x480x32 (5 9 1 2D) ; 2d_surf_mode: 0

After spending the better part of the day troubleshooting this I was able to get it to work by deleting the ops1.MIS file in the folder for my save. As far as I can tell the different MIS files for each floor contains either the current state of your player character or the current state of the level itself (probably way too simple of an explanation), so deleting the one that held the floor data reset the status of the floor to where it was when it first loaded including the SHODAN trigger and allowed me to continue.

How this will effect the game going forward I'm not sure, but it looks like these files are generated as you progress so I imagine it will just make a new file and be fine.

-unless you have manually saved into the autosave slot (on the very bottom of the menu), you will always have the autosave available.
-yes, deleting the mis file from the save will reset the level into its default state. ideally, you want to leave the level you are about to reset, save, and only then delete it from the new save.
-funnily enough, we would probably end up doing exactly this to fix your problem, while not generally recommended, it will be just fine in this particular situation.

but kind of too bad I couldn't get my hands on that save that was giving you trouble, would have been nice to check a thing or two and maybe find out what was up.