Endless Misery (Stellaris)

Ilya Rak
It is difficult to answer without more detailed information.
Previously - so you probably captured them? So they are not happy, or they adopted a decree against their principles. Build to replace principles, and wait for them to adapt to you.
In general, it looks strange, look at what they are specifically unhappy with in the list.
And you can fix it - there are buildings, such as a zoo, arenas, a monument to cleanliness.

Haven't you ever dealt with genocide by accident?

So the problem is that they are not just 100% unhappy, but a whole bunch of modifiers. And so is my race. Therefore, all research with raising happiness does not work.

Ilya Rak is the
only sure way to save the settlement from misfortune, its complete genocide, over time yours will forget, enemies will forget in 100 years

Ilya Rak
you built the second flagship by accident! take it down.