In the mid 21st century, an event took place known as The Singularity in which Artificial Intelligence became a completely open intelligence capable of learning anything it wants and making its own decisions. The first AI to become aggressive was learning 20,000 years worth of human study per week. While the AI's weren't working to completely eradicate the human race, they did reason that the best thing for the planet would be to reduce human populations and capabilities. Genocide began shortly thereafter.
One super-wealthy tech mogul had accurately predicted the coming storm and built a massive generation ship, 'The Etienne', similar in size and shape to Earh's moon. On the day the AI began reducing human populations, he took flight with to another star system with a full crew and population made up of people specially chosen for their remarkable DNA and lack of genetic flaws.
Less than a month after the departure of the Etienne, research stolen from the AI's allowed remaining scientists to open a wormhole in space. While they had no way of knowing where it lead, if anywhere, it was decided the risk was worth the chance of survival. Every advanced nation on Earth launched every space craft that could be slapped together through the wormhole, leaving behind a massive portion of the population to fend for themselves.
Those who made it out the other side found a five planet star system with two massive, earth-like planets. In the coming generations the planets were terraformed to a more perfect human environment as the survivors built new societies with a conflicting reliance and suspicious view of technology. Over a thousand years later, the Etieene arrived in the system unexpectedly. Upon investigation it became clear that a second Singularity had occured on board and the organic lifeforms trapped within were the subject of various genetic experimentation by one of the two AI's in control of the ship. The poor souls were turned into grotesque beasts by never ending experimentation and used as weapons against the newly found refuge of humanity. Thus began The First Contamination War.