The Outer Rim Coalition is a rebel organization that seeks to liberate the Outer Rim from the Earth System Alliance's control, but they are ill-prepared to fight against such odds. One day, the ORC's Scrap Springs Division manages to recover and reprogram Chronus-13, an ESA android with the ability to download Molarian code. At the same time, the ESA uses the Raxion II False Flag Operation from the previous game as a Pretext for War to wipe out all rebels on Infernis Prime, as well as to increase surveillance on the Outer Rim with the Zhelanov Array. The ORC must use Chronus-13 to take control of lost Molarian technology in order to stand a chance while discovering the secrets of this ancient civilization.
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This game contains examples of:
- Ambiguous Situation: The new ESA android, Andross-14, doesn't rat the party out despite sensing Zeron's original consciousness in Chronus-13. The party speculates that due to the second copy of Zeron in Andross, it may have been influenced by Zeron. However, Andross ends up becoming the next boss anyways, making it ambiguous how much control the second Zeron has over it.
- Artificial Stupidity: The enemy AI in Blackjack can choose to have two Aces become 11 each, resulting in an instant bust.
- Big Good: Played with. Commander Lexington is considered the leader of the Outer Rim Coalition rebel group, which the protagonists are a part of, but the coalition is also a decentralized group of autonomous cells. In the ending, he cedes leadership to Admiral Jaxon Bernard, who is more calm and levelheaded.
- Bittersweet Ending: Although the ORC drives the ESA off Infernis Prime, gets several interstellar nations on their side, and takes over the Zhelanov Array, Kern overloads Chronus-13 in the process and deleted most if not all traces of Chronus in the ESA's cyberspace. Worse yet, Kern used a data tap on the Supercarrier to determine the location of Time's Eclipse, which means the Order of Restoration isn't safe. However, Soren Xander continues to search for any traces of Chronus-13.
- Brain Uploading:
- Zeron is the only Molarian who managed to upload his mind into a Molarian computer, at least until it turns out over three hundred other Molarians uploaded their minds too. Zeron erased this from his memory so that even if he's captured or copied, his comrades won't be discovered. All of them are required to control the Molarian Supercarrier.
- Relnor is an associate of Trade Master Zurkt who tried to upload his mind into the Bank of the Alliance's cyberspace. Unfortunately, he got trapped in there long enough for his real body to die, and he can only exist digitally in Chronus-13's body.
- Kern has the Zhelanov Array, a massive satellite that allows his uploaded consciousness to exist in any cyberspace in ESA territory at once. This allows him to ambush Chronus-13 no matter where the latter dives into cyberspace.
- Crocodile Tears: During the ESA-hosted conference near the end of the game, INN anchor Byron Williams cries a river while broadcasting Alice Cromwell's speech, all to make the ESA look more sympathetic than it really is. He sheds further fake tears when the ESA takes credit for stopping the missile-launching wormholes that they set up.
- Dark and Troubled Past:
- Krax Grog's Geodonian community on Infernis Prime was captured by the ESA and put through deadly experiments, of which he was the only survivor. The ESA then enslaved him and put him in a digging site, but he eventually escaped and joined the ORC.
- Mari Williams and Jack Victor were kids on a contraband smuggling ship, but the ship was captured and their parents were arrested. Mari eventually found her mother, but the latter was brainwashed and no longer remembered her.
- Jianna Flux and Soren Xander were one of the few survivors of Scrap Springs, which tried to fight back against ESA occupation. The ESA wiped them out and Jianna only survived due to being converted into a cyborg. Jianna's father joined the ORC to atone for starting an unwinnable battle against the ESA, but he was killed in Moletown on a mission to free prisoners. However, the ending reveals her father was actually imprisoned, and she gets to reunite with him.
- Decoy Protagonist: The party leader is initially Mari, who leads the team in raiding a Molarian ruin. After the party defeats Chronus-13 and reprograms it to be loyal to the Outer Rim Coalition, Chronus-13 will be the party leader and viewpoint character.
- Digital Head Swap: During the conference with several prospective allies, the ESA is suddenly threatened by a red Molarian claiming to be Zeron, but this is actually Kern in disguise. When the Scrap Springs Division returns from the Bad Future, they remove the digital effects and expose Kern's charade to the other nations, causing them all to turn against the ESA.
- Even Evil Has Loved Ones: In the ending, Kern swears to bring someone back no matter what, while looking solemnly at a humanoid figure displayed on a screen. He turns off the screen the moment his subordinates enter the room, which shows how personal this task is to him.
- Evil Power Vacuum: Bernard is hesitant to expose Commodus's collusion with the ESA because this information would cause Canis Prime to be ravaged by a civil war between the various packs as each pack tries to install a new alpha. Unfortunately, his fears are proven true when Xena takes over Canis Prime by colluding with Novus Federation.
- Final Boss: The last boss is a security system that is remotely controlled by Director Kern.
- Final Solution:
- The Molarians discovered that the TRS Raven went back in time and nuked the populations of several planets in order to monopolize their technology, showing that they didn't simply stick to their mission of attacking the Calterans. The Molarians realized they were next and had to make their own preparations to thwart the ESA in the future as digital avatars.
- In the timeline where Scrap Springs Division leaves to find the Molarian fleet but doesn't come back in time, the ESA nukes all of Infernis Prime.
- The Friend Nobody Likes: The party and the Outer Rim Coalition are distrustful of Chronus-13, since it couldn't be completely reprogrammed and has the potential to switch back to its Earth Systems Alliance or Molarian programming. The ORC slowly gains respect for Chronus-13 once it gives them access to Molarian weaponry and overturns the ESA's advantage. In the ending, they mourn Chronus's death and seek to find any traces of it on the net.
- Go Mad from the Isolation: The Terran Republic officer, Hank Manson, was stranded on Xolarus III for over a decade. While he's sane enough to help the party, he also constructed a cat figure out of junk and believes this junk is a real cat.
- Hopeless Boss Fight: In Moletown's Operations Center, Chronus-13, Zeron, and Relnor dive into the mainframe, but Kern intercepts them. All of Kern's attacks deal enough damage to kill a party member several times over while he has 65000 HP, making it impossible to win. Afterwards, the party is forced to escape, but not before Kern copies Zeron's Molarian data.
- La Résistance: The Outer Rim Coalition is an insurgent group in Infernis Prime that opposes the Earth System Alliance's occupation.
- Magikarp Power: Purely robotic playable characters like T-17, Cerberus-7, and Kronos-5G cannot equip the same types of gear as other characters and their skill trees don't include passives to increase knowledge gain, which means they won't be able to learn new skills as fast as other characters, nor will they be able to abuse the best gear in the game. However, they can learn passives that allow them to act up to three times per turn, which puts them above characters that use Doppelganger armor.
- Memory Gambit: Zeron intentionally erased most of his memories and made himself believe that he's the only Molarian consciousness that can be downloaded. He knows the ESA will eventually find and copy his data, but the ESA doesn't know that they need 312 Molarians to control the Supercarrier. At the Molarian computer in the Vorago Dig Site, the other Molarians will not be downloaded unless Zeron's data accesses the computer for the second time, allowing Chronus-13 to download all the Molarians and gain exclusive access to the Supercarrier.
- Mind Hive: When the ESA has Chronus-13 attempt to hack a Molarian computer, the Molarian Intelligence Zeron enters Chronus's system. Later, Chronus has to download Relnor's digital consciousness because the latter's physical body is dead and he can no longer return to it. As a result, Zeron and Relnor fight alongside Chronus in cyberspace segments. In the Vorago Dig Site, Chronus-13 downloads all the other Molarian consciousnesses to help it control the Supercarrier. Finally, Chronus downloads the Molarian Sentinel from Xolaris III's weather tower.
- The Mole: The ORC's Echo Base is compromised by the traitorous Sampson, allowing the ESA to kill most of the troops there.
- Never Tell Me the Odds!: When the party learns Kern used the Eye of Providence to see the past, future, and other possible timelines, Soren asks what chance they have of beating him. Chronus-13/Zeron answers 27.9%, which the party isn't pleased to hear.
- The Quisling:
- Commodus is the current Alpha of the Canites on Canis Prime, but he colluded with the ESA to poison the previous Alpha Kronos. He also plans on forming an alliance with the ESA in order to get the ESA to free the Canites on other planets, but Lexington's party points out that the ESA cannot be trusted and that if they were really sincere about making peace with the Canites, they would have freed the other planets' Canites a long time ago.
- The Delta pack leader, Xena Delmonte, takes advantage of Lexington and Bernard's coup to side with Novus Federation instead and turns Canis Prime into a Puppet State for the federation while exiling all opposing factions.
- Redemption Demotion: Chronus-13 starts as the very first boss in the game and has over 3000 HP, making it difficult for the party to win without destroying the wires powering them. Once they do so, they bring Chronus bacak to an ORC base to repair and reprogram them. Afterwards, Chronus joins as a party member with about 700 HP and similar stats to the rest of the team.
- Tempting Fate: The OCR uses a camouflage field to hide in Scrap Springs, which the ESA already destroyed once. Many of the soldiers brag that the ESA won't go after this location again, but then the ESA's news announces that they'll do a more thorough sweep of Infernis Prime, putting the rebel hideout in danger of being discovered. In a bad timeline where the party couldn't make it back to the ESA's conference in time, the ESA nukes all of Infernis Prime, starting with Scrap Springs out of spite for it staying hidden for so long.
- The Scapegoat: This game's plot occurs in parallel to Origins, and it shows that after the Raxion II incident, Novus pinned the blame for the deadly gas on Carol Everson, even though it was an Earth Systems Alliance ship that did it.
- Unique Protagonist Asset: The android Chronus-13 is the protagonist of the game and has the ability to interact with Molarian code. This gives it the ability to control unmanned M1 Antimatter Tanks that the Molarians once used. Said tanks are actually more advanced than the ESA tanks despite coming from an ancient civilization. Later, Chronus downloads all the Molarian digital avatars and uses them to control the Molarian Supercarrier, a powerful ship that can teleport itself and allied ships across great distances.
- Xanatos Gambit: Kern would rather be the one to obtain the Molarian Supercarrier instead of the ORC, but he already prepared a contingency for if they obtain the ship. He knows the ORC will use the ship to save the Molarian fleet that got trapped in a black hole, so he has his own ships steal the anti-graviton device from the Molarians so that even if the ORC steals it back, they'll be stalled long enough by the black hole's time dilation that they won't be able to escape in time to win the war against the ESA. Worse yet, he also accounted for them using the Slipstream Gate, since he placed a data tap on the ship in order to trace their spacetime location, giving him the location of Time's Eclipse.
