Star Trek: 10 Times The Federation Was The Bad Guy
2. The Existence Of Section 31
We don't even need to delve into the murky misdeeds of Section 31, although there's probably enough material for a list of its own. The very fact it exists at all is enough to make us raise an eyebrow at the Federation.
Section 31 is a covert and independent branch of intelligence that deals with all things sinister, so the Federation doesn't have to. That very premise is flawed from the start. The Federation can't plead purity and light on the one hand, while holding a vial of poison in the other.
Plausible deniability isn't a good enough defence for a Federation that prides itself on taking the high road. Allowing an organisation to do its dirty work, by any means necessary, is still ethically bankrupt. Even if they choose to turn a blind eye to it.
On the contrary, it's arguably worse, because without any real oversight, Section 31's actions are fully capable of spiralling into the realms of villainy. And, oh wait, that's exactly what happened. On more than one occasion.
Rules, directives and values go out of the airlock when you have a gang of operatives at your back to make the difficult problems disappear, no questions asked.