- Complete Monster:
- Admiral Vlict Kenka is the governor of the Klingon colony Hrakkour. After a powerful being known as Quetzalcoatl comes to Hrakkour and starts spreading a pacifistic philosophy among the population, Vlict feels that the Klingons on Hrakkour have been corrupted by outside ideas and 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 blames Quetzalcoatl for the destruction of Hrakkou and puts him on trial. After Kirk demands Quetzalcoatl a fair trial and personally offers to go through some tests in an effort to defend Quetzalcoatl, Vlict designed the tests to kill Kirk and his crewmen.
- Dr. Ies Breddell was once part of the science council of Vardaine, a Federation colony, who held a grudge against Kirk since the day Kirk foiled Breddell's attempt to take over Vardaine. Joining a xenophobic anti-Federation movement on Vardaine and begining an operation to secretly construct starships modeled after the Federation star ships, Breddell creates his own version of the Enterprise and uses it to launch sneak attacks on Federation ships. Leading the fake Enterprise to attack the USS Republic and kill everyone on board, Breddell was seemengly killed in the battle against the real Enterprise. However, in the sequel Judgment Rites, it is revealed that he survived having been transported by a cloaked ship at the last moment. Even more obsessed with revenge after another defeat at Kirk's hands, Breddell secretly takes over a Federation space station studying a powerful anomaly. Creating a powerful weapon that uses the power of the anomaly, Breddell used it to destroy Earth, but the explosion causes a Federation ship to travel back in time and warn Kirk about this weapon right before the ship explodes, allowing Kirk to stop Breddell before he would have used his weapon.
- Disappointing Last Level: 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.
- Fanon: According to the information found in the ship's computer in each game, 25th Anniversary and Judgment Rites represent the events of the fourth and fifth years of the Enterprise's 5-year mission, respectively. Fans of the games typically consider this to be true, though neither of the games have ever been cited as canon in official discussions on the topic.
- Good Bad Bugs: In the fifth mission, it's possible to have the Klingon bad guy killed by a planetary Master Computer, 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.
- No Problem with Licensed Games: This game considered one of the best Star Trek games produced, and remains very faithful to the original series.
YMMV / Star Trek: 25th Anniversary