First HF - CD War

The CD declares war on the HF. They did this to prevent the HF alliance from spreading to other galaxies, to attack them while they were still weak.
  During the war, the HF population became victims of genocide at the hands of the CD. Although they eventually managed to hold the CD off, this came at a large cost. The HF would never quite recover.

The CD has captured many systems from the HF, some of which would be homeworlds. Most of these people were studied and killed, leading to quadrillions of deaths. The population of the entire HF was cut by almost an order of magnitude. This was a genocide on a huge scale from which the federation would never recover. It led to an increase in xenophobia which reduced the stability of the federation.
  The people of the HF saw that their lives were in danger, and they would be exterminated if this continued. They fought fiercely, but in a turn of events they began to deploy their more ethically questionable technologies during the war. The Hyperion Ethics Committee, too, saw this as the only way that the HF - and its people - can remain alive after the attack. When on the verge of death, the entire concept of ethics seems ridiculous.
  Now cleared to use weapons such as Trinity missiles, antimatter warheads, sound wave neutralizers, anti ship RKMs and more, the tide of the war began to turn. The HF would remain stable even after the war despite the use of this technology, but as the ethics committee began to re-establish requirements, the unethical technologies would be liquified. Some groups did manage to (illegally) keep some however, which damages the Federation.