Third Fleet
Third Fleet is the numbered fleet of which the Atlantis is the flagship. Commodore Kathryn Harper is the Commander, Third Fleet.
A common theme among the names of the ships of Third Fleet is early Earth spacecraft, scientists, and explorers.
Missing information below simply means that fact has not been established as of yet in our canon.
| Ship | Class | QSD | Commanding Officer |
| USS Atlantis | Sovereign | Yes | Commodore Kathryn Harper |
| USS Columbia | Sovereign | Yes | Captain Charles Finley |
| USS Discovery | Galaxy | Yes | Captain Ramón Esteban Valparaíso |
| USS Challenger | Galaxy | Yes | Captain Charlotte Grey |
| USS Endeavour | Prometheus | Yes | Captain Lydia Hawke |
| USS Odyssey | Odyssey | Yes | |
| USS Sovereign | Sovereign | Yes | Captain Bernadette Grey |
| USS Yeager | Galaxy | Yes | Captain Roderick Struan |
| USS Artemis | Luna | Yes | Captain Dianna Ricci |
| USS Apollo | Luna | Yes | |
| USS Galileo |
Luna | Yes | |
| USS Cassini | Luna | Yes | |
| USS Grissom | Nova | ||
| USS Shepard | Nova | ||
| USS Mercury | Akira | ||
| USS Gemini | Akira | Yes | Captain Steven Eagle |
| USS Soyuz | Akira | ||
| USS Viking | Intrepid | ||
| USS Pioneer | Intrepid | ||
| USS Voyager | Intrepid | ||
| USS Curiosity | Intrepid | ||
| USS Perseverance |
Intrepid | ||
| USS Ingenuity |
Nova | ||
| USS Sagan | Nova | ||
| USS Opportunity |
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| USS Spirit |
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| USS Sojourner |
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| USS Pathfinder |
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| USS Buran |
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| USS Mir |