The Terran Republic discovers a pair of crystals that can be used to travel through time and space, but when the TRS Dauntless uses one of the crystal travel to the future, they found that Earth was destroyed by a new alien faction, the Calterans. The TRS Raven then travels back in time to destroy the Calterans first, but the scientist commanding the Raven, Kern, secretly takes this opportunity to alter the timeline to one where Earth is the center of the Earth Systems Alliance, a brutal empire that he rules with an iron fist. The Dauntless crew is the only other faction that remembers the previous timeline, and now they must find allies to help them restore the timeline to its proper state.
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- Abusive Precursors: The First Ones were the first sentient beings in the universe, who gained control over time. Unfortunately, they used that power to start wars and destroy themselves, to the point of shattering time itself. Worse yet, the people of the present are in danger of repeating the First Ones' mistakes by abusing the latter's artifacts of time and space.
- Bait the Dog: Novus Federation seems like a potential ally to the Dauntless crew and the Novus Broadcasting Network's documentary paints them in a good light. However, Commodore Wellington orders the Dauntless not to restore their original timeline because it would undo the efforts of everyone in the current one. While this seems like a reasonable concern, Novus shows its true colors by ordering Captain Everson to abandon the Dauntless crew to the ESA's radioactive gas and imprisoning her when she refuses. Worse yet, they pinned the blame for the gas attack on Everson instead of on the ESA, making it clear that there's something rotten going on at the top of the federation.
- Can't Kill You, Still Need You: Colonel Thraxton passes up an opportunity to kill the Dauntless party because he knows they'll go back in the past and attempt to discover the secrets of Keldar, which will lead the ESA to Keldar's slipstream gate.
- Cybernetics Eat Your Soul: Commodore Wellington reveals that the scientist Kern was fatally injured in an assassination attempt and had his consciousness downloaded into an android body, but the process was imperfect and caused his mind to degrade.
- Early Game Hell: The first dungeon of the game is the ESA invading the TRS Dauntless, and there's no opportunity to shop for new equipment, making it difficult to deal with the enemies' high stats. Afterwards, the player has a chance to buy equipment upgrades from Nexus, but how much this help depends on how much money they managed to grind on the Dauntless.
- Evil Is Bigger: The TRS Raven under Kern's command is responsible for changing the timeline to one where the Terran Republic is turned into the tyrannical Earth Systems Alliance. The Raven is also bigger than its sister ship, the TRS Dauntless, which is under the party's control. As a twist, during the time skip, the original Dauntless crew takes control of the Raven while the ESA steals the Dauntless, which inverts the dynamic. However, during The Stinger, an unknown faction steals the Dauntless from the ESA.
- Final Boss: In the Keskus Labyrinth, the final enemy the player faces is Keldar, who seeks to test the party's worthiness in helping to prevent the Purge.
- Hero Antagonist: The Final Boss, Keldar, fights the party to determine if they're worthy of helping his Kryll faction save the universe from the Purge. Once they do so, he allows them to use the slipstream gate to join his comrades in Time's Eclipse in the Bad Future.
- Horrifying the Horror: The light and darkness are primordial cosmic entities that have been in conflict since the start of the universe. They are terrified of the First Ones and their potential to control time, so much that they formed a truce and went into hiding until the First Ones destroyed themselves with their own time powers.
- Never My Fault: Commodore Wellington blames the Dauntless crew for the disastrous mission to recover the Raven and for the ESA gassing Raxion II, even though it was his Novus Federation forces who failed to stop the gas ship.
- Schmuck Bait: The Novus soldiers note that Raxion II has a suspicious lack of guards despite it being an important location for the ESA. This is because the ESA always planned to let Novus take the planet, only for them to unleash radioactive gas on the planet and kill everyone, including ESA civilians. They then frame Novus Federation for this atrocity in order to win the propaganda war.
- Sentient Cosmic Force: The light and darkness of the universe have been in conflict since the start of the universe, but formed a truce because of the threat of their accidental creations' time powers.
- Spy Speak: When the Dauntless crew is placed under Novus Federation command, Captain Carol Everson and Lieutenant Magnus Archer designate a code word, "Groundhog," to indicate when they are in an emergency situation that can compromise their chain of command. During the Raxion II mission, Carol uses it to indicate that Archer should prioritize her orders over Novus and escape with the Raven.
- Teeth-Clenched Teamwork: The Dauntless crew isn't pleased with the Novus Federation forcing them to give up on going back to their original timeline, and are only teaming up because of their mutual enemy in the ESA. This comes to a head when Captain Carol Evers orders the Dauntless crew to do a blind jump with the Raven in order to escape the ESA's radioactive gas, against the Novus Federation's orders. Afterwards, the Federation imprisons Carol for insubordination and blames the mission's failure on her.
- Time Skip: After the Raxion II mission, Captain Carol Everson spends five years in Novus Federation's prison before her allies teleport her to Kelvik IV. For Archer's party, it was actually twenty-five years because they used the TRS Raven to travel back in time before reuniting with Everson in the present.
- Yin-Yang Bomb: The First Ones were accidentally created from the conflict between the light and darkness, resulting in them having power over both.
