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The star navigational map from the United Federation of Planets

When ready to warp to another star system, ask Chekov to show the navigational map (hotkey  N ) and decide the next destination. The game has 44 star systems available, with only 20 of them being identified in the manual and detailed on the library computer. From those, only some are visited during the game, others having no purpose in the game other than training with random encounters. But as there is a chance of too many enemies appearing and overwhelming the Enterprise, it is better to be avoided due to the danger. Each system has one of its planets visible as soon as the Enterprise arrives.

Systems

1 1 Centurius
Optional. A system on the edge of the Romulan/Federation Neutral Zone. Centurius III was once inhabited, but its colony was destroyed in the first Romulan-Federation war. The planet is now uninhabitable due to radiation levels.
2 2 Cameron's Star
Optional. A Federation world, first colonized by the explorer Todd Cameron. It is the site of some of the finest learning centers in the Federation.
3 3 ARK7
ARK7 (also written as ARK-7) is a research station and a highly sophisticated Arcology project looking into the origins of life in the universe. The third scenario, Love's Labor Jeopardized, takes place here. The station is only visible when in orbit during the scenario, and the planet visible in this system is similar to the one in the Alpha Proxima system.
4 4 Harlequin
The first star system from the fourth scenario, Another Fine Mess. Also, the final battle happens near Vardaine, the third planet in the system. This star system has two inhabited worlds, Harlequin-3 (Vardaine) and Harlequin-5 (Aloysia). Vardaine is an Earth colony that has been involved in controversy more than once. Aloysia is non-Federation world heavily influenced by Elasi pirates. Vardaine's appearance is similar to the planet in Harrapa.
5 5 Harrapa
The second star system from the fourth scenario, Another Fine Mess. A binary system whose fourth planet is the inhabited Class M world Chameleon. Chameleon was dominated by Elasi pirates and is struggling to break free of their influence.
6 6 Elasi Prime
Optional. Elasi Prime is a binary star system, whose one inhabited planet, Menalvagor, is currently undergoing a revolution. The Elasi pirates come from this system. The visible planet (possibly Menalvagor) is similar to Pollux V.
7 7 Digifal
This is the first system from the fifth scenario, The Feathered Serpent, located near the Klingon Neutral Zone. Digifal contains two habitable planets, Digifal III (Zamphor) and Digifal IV.
8 8 Strahkeer
Optional. A Klingon world in the disputed Klingon-Federation Neutral Zone.
9 9 Hrakkour
This is the second system from the fifth scenario, The Feathered Serpent. Hrakkour IV is a world in Klingon space, which has belonged to their Empire for at least four generations, governed by the Kenka family.
10 10 Tri-Rho Nautica
Optional. A Federation world near the Klingon Neutral Zone.
11 11 Shiva Omicron
Optional. A star system in Federation space. Shiva Omicron IV began the preliminary negotiations to join the Federation.
12 12 Alpha Proxima
The scenario That Old Devil Moon happens on Scythe, an asteroid that used to be the moon of Alpha Proxima III (Proxtrey). This system has five planets, with two being inhabited.
13 13 Omega Maelstrom
Optional. An uninhabited system with proto-planetary debris scattered throughout the plane of the elliptic. It appears that pirates are using abandoned industrial sites as hideouts.
14 14 Argos IV
Optional. A system in Federation space with a major scientific institute.
15 15 Beta Myamid
The second scenario, Hijacked, takes place near Beta Myamid VIII, a Federation world. A supply depot orbiting Beta Myamid VIII has been subject to attacks from Elasi pirates.
16 16 Sirius
Optional. The brightest star visible from Earth. There are no inhabited planets in the Sirius system.
17 17 Sigma Zhukova
According to the cluebook, this trinary star system is the starting point, where the mock combat exercise with the U.S.S. Republic happens. Note that the planet visible during the mock battle (pictured in the bridge screenshot above) is different from the one seen when haphazardly travelling to the system.
18 18 Castor
Optional. A binary star system with several inhabited worlds. Castus (Castor-B IV) is a prime mining site for the Andorian Mining Consortium (AMC).
19 19 Pollux
The first scenario, Demon World, takes place in Pollux V, an inhabited satellite of Pollux-B that emerged from an ice age caused by large meteor strikes. It has recently been colonized by the Acolytes of the Stars.
20 20 Christgen
Optional. Christgen 3 is an important center of diplomacy in the Federation. The cluebook mentions that the Enterprise was going on a mapping survey in this system after the mock combat, but the mission was postponed for an emergency in Pollux V.
N/A Other systems
Optional locations that have no relation to any of the game's missions, so there is no logic reason to visit them. Their visible planets appear to have the same appearance as the others above.