** Though most [[ProudWarriorRaceGuy Klingons]] have a code of honor that makes them sympathetic, [[InsaneAdmiral Admiral]] Vlict Kenka takes his to [[KnightTemplar a terrifying extreme]]. Vlict was the governor of the Klingon colony Hrakkour . A [[SufficientlyAdvancedAlien powerful being]] known as [[Myth/AztecMythology Quetzalcoatl]] comes to Hrakkour and starts spreading a pacifistic philosophy among the population. Feeling that the Klingons on Hrakkour have been corrupted by outside ideas, Vlict orders everyone on Hrakkour to be killed, including his own family. Realizing he has gone far beyond his orders to deal with the situation and wanting to avoid punishment from the Klingon High Council for his genocidal crimes, Vlict [[NeverMyFault blames Quetzalcoatl]] for the destruction of Hrakkou and puts him on [[KangarooCourt trial]]. Kirk demands Quetzalcoatl be treated fairly by the trial and personally offers to go through some tests to prove his own worthiness as a warrior, in an effort to defend Quetzalcoatl. However Kirk soon discovers that these tests are designed to kill Kirk and his crewmen, so that Vlict will no longer have to deal with Kirk's inference.
** [[MadScientist Dr. Ies Breddell]] was once part of the science council of Vardaine, a Federation colony. A young Kirk foils Breddell's plan to take over Vardaine and he has held a grudge against him ever since. A decade later Breddell has joined an xenophobic anti-Federation movement on Vardaine and begins an operation to secretly construct star ships modeled after the Federation star ships. Breddell creates his own version of the [[EvilKnockOff Enterprise]] and uses it launch sneak attacks on Federation ships. The fake Enterprise attacks the USS Republic and kills everyone on board. After the real Enterprise defeats the fake Enterprise, Breddell is seemingly killed, only to return in [[VideoGame/JudgmentRites the sequel]].
* DisappointingLastLevel: The final mission in the release version gives you a two-room mission on the USS ''Republic'', followed by a ludicrously hard fight with a Vardaine copy of the ''Enterprise''. The CD version expands this to a much bigger mission on the ''Republic''.
* GoodBadBugs: In the fifth mission, it's possible to have the Klingon bad guy killed by a planetary MasterComputer, then act like a jerk toward his subordinate, leading to a battle between the ''Enterprise'' and a Klingon ship. After winning the battle, Spock reports Kirk's actions to Starfleet Command -- but in an apparent oversight by the developers, this won't result in any reduction to the mission score, giving the impression that Starfleet are actually quite happy to have their captains going around starting fights with the Klingons.
* NoProblemWithLicensedGames: This game considered one of the best ''Franchise/StarTrek'' games produced, and remains very faithful to the original series.