| Department | Name | Registry | Class | Commanding Officer |
| C-in-C | USS Mississippi | NCC-1959 | Sovereign (SC) | Admiral Rowdy Randy |
| C-in-C | USS Tirpitz | NCC-1227 | Sovereign (SC) | Captain Seth Gideon |
| ----- | | | | ----- |
| Academy | USS Night Hawk | NCC-94924 | Intrepid | Vice Admiral Galaxy DeLanet |
| Academy | USS Excelsior | NCC-20001 | Excelsior mkIII | Captain Ken Sulu |
| Academy | USS Firestarter | NCC-2208 | Nebula mkII | Flt. Capt. Joseph Travis |
| Academy | USS Edward Jenner | NCC-74659 | Intrepid mkII | Captain Trinity Mikhael |
| Academy | USS Okuda | NCC-94132 | Sovereign | Captain Lexa Zahn |
| Academy | USS Columbia | NCC-91099 | Defiant | (training vessel) |
| Academy | USS Diablo | NCC-87650 | Miranda | (training vessel) |
| ----- | | | | ----- |
| IA | USS Spectre | NCC-65142 | Steamrunner | Admiral Grand |
| IA | USS Bellerophon | NCC-2117-B | Sovereign | Admiral T'chal |
| IA | USS Arista | NCC-2505 | Prometheus | Vice Admiral Ron Wallis |
| IA | USS Guardian | NCC-91526 | Intrepid | Captain C'Thia |
| IA | USS Angel | NCC-63945 | Akira | Admiral Selern |
| IA | USS Sunset | NCC-98224 | Excelsior mkII | Commodore Amy Star |
| IA | USS Shenandoah | NCC-96875 | Excelsior mkIII | Commodore Alex Sherman |
| IA | USS Avalon | (unknown) | Ambassador | Captain Richard Sherman |
| IA | Psi Base | | | Admiral Selern |
| IA | Chi Base | | | Admiral Grand |
| IA | USS Phantom | NCC-9000-B | Intrepid | Rear Admiral Evek |
| IA | USS Mercury | (unknown) | Sabre | (unknown) |
| IA | USS Phantasm | (unknown) | Steamrunner | (unknown) |
| ----- | | | | ----- |
| ExA | USS Bismarck | NCC-1226 | Sovereign | Admiral Adam Vanderheiden |
| ExA | USS Antares | NCC-979386 | Sovereign | Vice Admiral William Riker |
| ExA | USS Sanushi | NCC-10903 | Sirius | Commodore Jessica Zar |
| ExA | USS Infinity | (unknown) | Intrepid | Admiral Janelle |
| ----- | | | | ----- |
| Intell | USS Frontier | NX-74356 | Frontier | Commodore AJ Lawrence |
| Intell | USS Benedict | NCC-95433-A | Sovereign mkIII | Commodore Rachel se Ranor |
| Intell | USS Grandmarie | NCC-13048 | Intrepid | Rear Admiral Jaana Lasko |
| Intell | USS Saratoga | NCC-32095-A | Galaxy | Captain Alison Krennick |
| Intell | USS Athena | NCC-78326 | Sovereign mkIV | Captain Samatha Dillon |
| Intell | USS Rutherford | NCC-1432-D | Prometheus | Commodore Tracy Phelan |
| Intell | USS Vengeance | NCC-74321 | Sovereign | Captain Mike A. Boyer |
| Intell | USS Falconeye | NCC-12637 | Intrepid | Captain Cyber Wulfe |
| Intell | USS Brandenburg | NCC-78359 | Sabre | Captain Jerry Banks |
| Intell | USS Silent Shadow | NX-7403 | (unknown) | Rear Admiral Tapestry Valenza |
| Intell | USS Aysha | NCC-108010 | Galaxy mkII | Captain Carry Manchester |
| Intell | USS Alabama | NCC-3022 | Prometheus | Rear Admiral Sylvester Wolf |
| Intell | USS Ghost Ranger | NCC-17101 | Sovereign | (unknown) |
| Intell | USS Antarctica | NCC-71925 | Defiant (Hazard) | Commodore Erutan Jaxon |
| ----- | | | | ----- |
| Ops | USS Camarilla | NX-1711 | Camarilla | Lt. Gen. Brandis Marceau |
| Ops | USS Andromeda | NX-78355 | Andromeda | Captain Neko Gideon |
| Ops | USS Alexander Hamilton | NCC-88829-A | Sovereign mkIII | Commodore Sh'del Ranger |
| Ops | USS Sidewinder | NCC-3300 | Steamrunner | Commodore Andrew Pethel |
| Ops | USS Saint | NCC-4077 | New Orleans | Commander Jasen Roland |
| Ops | USS Oklahoma | NCC-78978 | Intrepid mkII | Lt. Commander Tammy Ross |
| Ops | Starbase Windsor | | | (unknown) |
| Ops | Utopia Planitia | | | Commander Jasen Roland |
| Ops | San Francisco | | | Commander Jasen Roland |
| Ops | Alpha Lyrae | | | Lt. Commander Tammy Ross |
| Ops | Beta Antares | | | Commodore Sh'del Ranger |
| ----- | | | | ----- |
| SFSMC | USS Nightingale | NCC-1900 | Intrepid mkII | Rear Admiral Jacen Antilles |
| SFSMC | USS Defiance | NCC-0197-A | Defiant | Admiral T'Chrissta Ra |
| SFSMC | USS Wallace | NCC-88835 | Intrepid mkII | Captain Savin |
| SFSMC | USS Ayres | NCC-3020 | Olympic | Admiral Jennifer Penfield |
| SFSMC | USS Slavic | (unknown) | Nova | Captain Dylan Storm |
| SFSMC | USS Voight | NCC-10812 | Norway | Captain Hannah Saloi |
| SFSMC | USS Allegiance | NCC-17998 | Norway | Commander Aram Na'aa |
| SFSMC | Starbase Versailles | | | Commander Aram Na'aa |
| ----- | | | | ----- |
| MilOps | USS Arkhammer Exodus | NX-51853 | Sovereign mkIV | Admiral Herby McWarren |
| Intell | USS Eclipse | NX-78352 | Eclipse | Vice Admiral Chad Phillips |
| MilOps | USS Maverick Zero | (unknown) | White Star | Admiral Jim Raynor |
| MilOps | USS Rapture | NCC-2513 | Frontier | Vice Admiral Iceni Dillon |
| MilOps | USS Bonaventure | NCC-3229-B | Prometheus | Commodore Tavell Manchester |
| MilOps | USS January | NCC-74686 | Intrepid | Commodore Tom10342130 |
| MilOps | USS Blade | NCC-27044-A | Galaxy mkIII | Bgdr. Gen. Ameris Zarek |
| MilOps | USS Darksun | NCC-86212 | Sovereign mkII | Vice Admiral Marisa se Ranor |
| MilOps | Fort Ticonderoga | | | Captain Elishabetha Verichi |
| MilOps | USS Warhammer | NCC-108106 | Cyclonus | Vice Admiral Syke Matrix |
| MilOps | USS Maverick | NXP-501986 | Defiant (mod) | Vice Admiral Jim Raynor |
| ----- | | | | ----- |
| SFSF | USS Republic | NX-9215 | Republic | Rear Admiral Billy Blaze |
| SFSF | USS Black Widow | NCC-91116 | Sovereign mkII | Commodore Mason Storm |
| SFSF | USS Vimy Ridge | NCC-68364 | Akira mkII | Commodore Jack Carter |
| SFSF | USS Macross | NCC-12010 | Defiant | Captain Amulek de Vega |
| SFSF | USS Essential | (unknown) | Cheyenne | Captain Gen Manath |
| SFSF | USS Reckoning | (unknown) | Republic | Colonel Gregory Helms |
| SFSF | USS Lexington | NCC-2864 | Akira | Captain Raszia Sherman |
| SFSF | Starbase 1 | | | (unknown) |
| SFSF | Deep Space Five | | | (unknown) |
| SFSF | Skunkworks | | Shipyard | (unknown) |
| SFSF | USS Yorktown | NCC-1717-D | Frontier | Rear Admiral Kyle Roberts |
| SFSF | USS Prism | (unknown) | Nova | Captain Gen Manath |
| SFSF | USS Resurrection | NX-34317 | Resurrection | Captain Jody Hammerhand |
| SFSF | USS Blaze of Glory | NCC-2525-B | Defiant | (unknown) |
| ----- | | | | ----- |
| Omega Fleet | USS Sirius | NCC-93021 | Sirius | Commodore Brian A. Medra |
| Omega Fleet | USS Mar Sara | NCC-94422 | Nova mkII | Flt. Capt. T'Lana Chamrajnagar |
| Omega Fleet | USS Chamberlain | NCC-26542-A | Ambassador | Captain Karyn Sullivan |
| Omega Fleet | USS Camelot | NCC-94681-A | Sovereign mkIII | Captain Tavian Nichols |
| Omega Fleet | USS Crimson Devil | NCC-100900 | Steamrunner | Captain Steven Metings |
| Omega Fleet | USS Cygnus | NCC-3021-B | Akira | Captain Robert Chamrajnagar |
| Omega Fleet | USS Blackwell | NCC-711871 | Olympic | Captain Patricia Latham |
| Omega Fleet | USS Edmonton | NCC-10950-A | Sovereign mkIII | Captain Marc Bordeaux |
| Omega Fleet | USS Jackson Hill | NCC-76103 | Excelsior mkIII | Captain Amber Langley |
| Omega Fleet | USS Nemesis | NCC-55806 | Sovereign mkIII | Rear Admiral Syke Matrix |
| Omega Fleet | USS Witham | NCC-8952 | Defiant | Captain SJM Pagrashtak |
| Omega Fleet | Omega Prime | | | Commodore Brian A. Medra |
| Omega Fleet | Starbase Omni | | | Flt. Capt. T'Lana Chamrajnagar |
| Omega Fleet | USS Montclair | NCC-100901 | Cyclonus | Captain Kinaka Holra |
| Omega Fleet | USS Pathfinder | NCC-96116-A | Pathfinder | Lt. Commander Thomas Paris |
| ----- | | | | ----- |
| Epsilon Fleet | USS Nefertiti | NCC-82137 | Excelsior mkIII | Commodore Krystal Ross |
| Epsilon Fleet | USS Brazen | NCC-8001 | Saber | Captain Clissa Boyton |
| Epsilon Fleet | USS Nathan Hale | NCC-85454-A | Sovereign mkIII | Captain Janni Seln |
| Epsilon Fleet | USS Georgetown | (unknown) | (unknown) | Captain Sarah Barker |
| Epsilon Fleet | USS Equinox | (unknown) | Excelsior mkIII | Captain Robert Drake |
| Ops/Antares | USS Empyrean | NCC-78725 | Frontier | Captain Will Taylor |
| Epsilon Fleet | USS Crown Victoria | NCC-91701-IX | Prometheus | Captain Zialandria*Zan |
| Epsilon Fleet | USS Tornado | NCC-57250 | Akira mkII | Captain Kurt Matson |
| Epsilon Fleet | Epsilon Prime | | | Captain Clissa Boyton |
| Epsilon Fleet | Fort Charleston | | | Commodore Krystal Ross |
| Epsilon Fleet | USS Coral Sea | NCC-88827 | Sovereign mkIII | Commodore Corran Phillips |
| Epsilon Fleet | USS Apollo's Revenge | NCC-91021 | Galaxy | Epsilon Security |
| ----- | | | | ----- |
| Sierra Fleet | USS Pathfinder | NX-96116-A | Pathfinder | Commodore Scott Matson |
| Omega Fleet | USS Crown Jewel | NX-50750 | Cyclonus | Captain Ryan Stone |
| Sierra Fleet | USS Gettysburg | NCC-74003 | New Orleans | Rear Admiral Shannon Murphy |
| Sierra Fleet | USS Indiana | NCC-7003 | Defiant | Commodore Kerry Sullivan |
| Sierra Fleet | USS White Wolf | NCC-91081 | Sovereign mkIII | Captain Sivak |
| Sierra Fleet | USS Nichols | (unknown) | Defiant | Commander Felicity Rekca |
| Sierra Fleet | USS Scorpio | NCC-78532 | Steamrunner | Commander Robert Blaze |
| Sierra Fleet | USS Greywolf | NCC-98715 | Akira mkII | Colonel Randy Oroton |
| Sierra Fleet | USS Fearless | NCC-4598 | Nebula | Captain Kalia Storm |
| Sierra Fleet | USS Nightshade | (unknown) | Sovereign | Captain Tam Stevens |
| Sierra Fleet | USS Talon | (unknown) | Defiant | Captain Kevin Royal |
| Sierra Fleet | Sierra Prime | | | Captain Kevin Royal |
| Sierra Fleet | USS Stewarts | NCC-25839 | Defiant | Commander Felicity Rekca |
| Sierra Fleet | USS Tempest | NCC-1459 | Intrepid | Commodore Elise Shavonne |
| ----- | | | | ----- |
| Alpha Fleet | USS Shadowcat | NCC-1805 | Sovereign | Commodore John Yocum |
| Alpha Fleet | USS Aldebaran | NCC-83101 | Intrepid | Flt. Capt. Andrew Ullery |
| Alpha Fleet | USS Connecticut | NCC-06443 | Resurrection | Captain T-8725 |
| Alpha Fleet | USS Gallant | (unknown) | Intrepid | Captain Jon Snow |
| Alpha Fleet | USS Avenger | NCC-74698 | Intrepid | Captain Jaclyn Murphy |
| Alpha Fleet | USS Orlando | (unknown) | (unknown) | Captain Simran Manchester |
| Alpha Fleet | USS Xavier | NCC-7356 | Sovereign | Commander Casper Sett |
| Alpha Fleet | USS Duke | (unknown) | Galaxy | Commander John Wayne |
| Alpha Fleet | Alpha Prime | | | Captain Jon Snow |
| Alpha Fleet | Centura 6 | | | Captain Harris Porter |
| Alpha Fleet | USS Sunstorm | NCC-42578 | Prometheus | (unknown) |
| ----- | | | | ----- |
| Ops/Windsor | USS Rutledge | NCC-57295 | New Orleans | |
| Ops/Windsor | USS Aries | NCC 72805-A | Sovereign mkII |
| Ops/Windsor | USS Venture | NCC-59885 | Galaxy |
| Ops/Windsor | USS Midway | NCC-78923-A | Sovereign mkII |
| Ops/Windsor | USS Persephone | NCC-27270-A | Akira mkII |
| Ops/Windsor | USS Hellfire | NCC-60000 | Nebula mkII |
| Ops/Windsor | USS Pioneer | NCC-91095 | Sovereign mkII |
| Ops/Windsor | USS Vulcans Forge | NCC-???? | Galaxy | |
| Ops/Windsor | USS Jupiter II | NCC-10824 | Sovereign mkIII |
| ----- | | | | ----- |
| Ops/Antares | USS Surak | NCC-65601 | Excelsior mkIII |
| Ops/Antares | USS Cypress | NCC-93024 | Intrepid |
| Ops/Antares | USS Pegasus | NCC-53847 | Oberth |
| Ops/Antares | USS Cauldron Born | NCC-2552 | Intrepid mkII |
| Ops/Antares | USS Nightsun | NCC-31004 | Centaur |
| Ops/Antares | USS Tazmania | NCC-78535 | Cyclonus |
| Ops/Antares | USS Tercel | NCC-78537 | Nova mkII |
| Ops/Antares | USS Banshi | NCC-82345 | Intrepid mkII |
| ----- | | | | ----- |
| Ops/Durani | USS Valor | NCC-44444 | Steamrunner |
| Ops/Durani | USS Thomas Jefferson | NCC-44425 | Akira mkII |
| Ops/Durani | USS Phantom Spirit | NCC-85000 | Sovereign mkIII |
| Ops/Durani | USS Patrick Henry | NCC-74659 | Intrepid mkI |
| Ops/Durani | USS Horizon | NCC-65980 | Galaxy |
| Ops/Durani | USS Alexander | NCC-108221 | Akira mkII |
| Ops/Durani | USS Hornet | NCC-76654 | Norway |
| Ops/Durani | USS Indomitable | NCC-108069 | Galaxy |
| Ops/Durani | USS Venture | NCC-59885 | Galaxy |