Although all colonies fell quickly into line with this decree, the populations of these solar systems were taken completely for granted by the Earth Empire. For centuries, honoring their word and fulfilling all duties demanded of them, the colonists were treated with nothing but spite, and branded as second-class citizens. Eventually, people throughout many colonies and across dozens of planets, specifically those of the Gallonigher System, began to voice their protests and disdain at the Empire's harsh treatment. The Tzar, believing the outer-system colonists to be little more than peasant scum, became enraged that his subjects would even dare to question their duties to the Empire. Deciding quickly to have the protests suppressed, the Tzar moved his massive fleets to the outer systems, where he ordered the annihilation of every city that had so far reported even minor protests.
Believing that his subjects wouldn't ever dare to question their places again, the Tzar rallied entire systems into open revolt through his actions - even alienating many of his most loyal and experienced outer-system Naval officers, who quickly defected to the faction leading the most passionate anti-Empire efforts, The League Of Free Worlds. Due to these events, The League went from being a minor political annoyance, to becoming the most dangerous military threat posed to the Earth Empire's rule. The Tzar, now with a lack of experienced fleet officers in the outer systems, placed a young and arrogant Admiral in charge of a massive Imperial taskforce and dispatched it to destroy 'The Father' and the large League fleet growing and amassing strength in the Gallonigher System. Although only in command of obsolete fighters and small to mid-sized capital ships, 'The Father' and his advisors drew the complacent Navy fleet and its inexperienced officers into ambush, obliterating the entire taskforce with very few losses to their own forces. The Battle Of Benay served as the League's rallying call to the colonies, and as League supporters and Navy loyalists wage civil war across the known systems, The League Of Free Worlds begins its push towards the Sol System, Earth and the Tzar.colonist, in the service of "The Father" and the rapidly expanding "League Of Free Worlds" resistance movement. The player is thrust into the action following The League's miraculous victory at the Battle of Benay. As a skilled League fighter pilot, the character must struggle to overcome the oppressive Earth Empire and its massive naval fleets across several star systems embroiled in civil war. The character is tasked with multi-role assignments, consisting of perimeter defense, guarding supply lines, protecting capital fleetships, dogfighting against advanced Navy fighters, infiltrating Imperial territory and obtaining Naval technology. Unlike most video games, failure of a mission (or even several) does not necessarily cause the game to end. Colony Wars features a branching system with many separate endings, depending on the player's rate of success/failure; even losing every consecutive mission from the beginning of the game will result in the player "finishing" the title, albeit with dire consequences for the game's protagonist. Colony Wars, Mertens and the newly united Sol fleet, under the guidance of their charismatic leader, Kron, are bent on revenge for the Navy's defeat. Battling vast League fleets, battle-hardened elite mercenaries and alien opponents across unfamiliar and hostile territory, Mertens soon discovers that all is not as it seems within the heart of the Navy, and that the most dangerous of enemies are, in fact, not his enemies at all. Colony Wars: Vengeance features a "tech token" upgrade system, which allows the player to boost the combat prowess of each of Mertens' various fighters used throughout gameplay. Tokens can boost a fighter's shields, engines, firepower and hull strength, allowing the player to convert even the most basic fighter into a formidable weapon, provided the required number of tokens are available. The branching feature of the original title is also featured in Colony Wars: Vengeance. Colony Wars: Red Sun places the player in the role of Valdemar, a miner turned mercenary, during the "Vengeance Wars." It expanded on the "tech token" upgrade feature of Colony Wars: Vengeance by allowing players to buy fighter craft, upgrades and new weaponry from money (or credits as they were called in-game) earned on missions. It also introduced alien interaction into the storyline, which had previously focused almost entirely on the League/Navy conflict with little more than minor comments regarding the status of the civilian/neutral populations throughout the war. Valdemar is able to accept missions from anybody capable of providing the money, and can often choose from several mission at any given time. Clients include pirates, conglomorates, security forces and both The League Of Free Worlds and the Colonial Navy. Of all three characters, Valdemar is of the greatest importance, as his journey ultimately leads him on a desperate race to rescue the human species from complete destruction, whereas the first two titles, and the characters featured, focused entirely on the League/Navy war. Colony Wars: Red Sun was criticised for the removal of the branching system featured in both Colony Wars and Colony Wars: Vengeance, which many fans considered a unique and impressive characteristic of the series. The ability to view cinematics was also removed, which was also perceived as another drawback to the title.
Over the centuries, the brutal regime gained opposition, and the League of Free Worlds was formed out of insurgency against the Empire, led by a figure known as "The Father". The first conflict can be analogised in the form of the Vietnam War, as the mighty and powerful Navy are drawn to the edge of defeat by a smaller and under-equipped force.
Assuming that Vengeance is the official continuation of the timeline (as there are multiple endings depending on player progress, creating a similar illusion of free choice as seen at the end of Half-Life), the Navy push the League forces out of the Sol System. But in their retreat, the League destroy the free orbiting space platform that tethered the wormholes from each system, meaning the Earth Empire and the Navy are effectively trapped. The now almost sterile Sol System plays host to a civil war between Navy factions, with the League left to wonder the fate of their enemies.
After an undisclosed number of years (suggested to be approximately one hundred as stated by ace League fighter pilot, The Widowmaker), the civil war is drawing to a close with the emergence of a new leader, known as Kron. It is still the 5th millennium (as stated by Valdemar in Colony Wars: Red Sun) and the Navy has united enough of the populace to become a military force once again. Though nothing of its former power, they embark upon a campaign of retribution against the League of Free Worlds, who have now become as corrupt as the Earth Empire once was. But as they progress in their campaign, it becomes clear that the initial reasons for the breakout from Sol were nothing but a sham, with the entire reasons for the war being lost in mutual fear and need, as both the Navy and League come under attack from a hitherto unknown and mysterious alien race. As they fight off the attacks, the Navy commander, Kron, attempts to continue his campaign against the League, eventually fighting the Navy itself. As it transpires, Kron was once a highly regarded League loyalist, who was deliberately sent on a suicide mission to Earth in the previous war due to his unstable nature. The entire 2nd Colonial War was built on his personal vendetta he felt the need to fulfil. In the end, Mertens kills Kron, leaving his remaining loyalists to surrender to the now united League and Navy Factions, as it is also Mertens (the player) who closes the alien wormhole, preventing more incursions.