The Sisko and The Maquis. (Spoilers ahead)

This post is about the Maquis story arc on Deep Space Nine. Consider it a primer for all things Maquis. The post assumes, that many have already followed the story arc from the tv show.

Much of the story is here at Memory Alpha, too.

The people who eventually became the Maquis, were supposed to be aware of the fact, that the border worlds might become disputed territories again, as they previously were in the first place. Alas, the Maquis weren't.

Maybe it was, that the Federation failed to communicate this to the Maquis, or expected them to be intelligent enough to follow the treaty.

The Maquis' initial presence on border territories was supposed to indicate, that the Federation were serious about digging their heels in.

After the Federation–Cardassian peace treaty (and Cardassia conceding Bajor), the territories at the time belonging to the Maquis were ceded to Cardassia. I'm sure there was a fair bit of horse-trading at the talks, because Cardassia wasn't a particularly resource-rich planet, but they had earlier invaded the wrong one (Bajor).

Although the Maquis were assured, that they would be treated well in the Cardassian Union, they weren't.

The Maquis as an organisation was formed, and they put the Federation into a very uncomfortable place with this, because Cardassia was then in a position to accuse the Federation, that it wasn't honoring the treaty.

From this impossible situation, Sisko found a very clever resolution; to smoke out the remaining Maquis civilians from their last major outpost (Solosos III) and capture Michael Eddington in order to fulfill the treaty, he had the ecology of that world destroyed, making it simultaneously very expensive—or even almost impossible for the Cardassians to clean up that planet.

Well, they could have cleaned up the climate of that planet, but restoring its ecology to its previous pristine (or primordial) state became practically impossible. So, the Cardassians did get their cake (per treaty), but could not eat it. Anymore.

Essentially, a scorched-earth policy.