Eddington: Tell me, Captain, what is it that bothers you more: the fact that I left Starfleet to fight for a higher cause or the fact that it happened on your watch?
The Bad Guy Wins: Discussed in the end by Sisko and Dax, as he opted to play the role of villain to Eddington's hero.
Dax: Sometimes I like it when the bad guy wins.
Cruel Mercy: In The Teaser, Eddington prevents Sisko's meeting with an informer. Eddington balks at the suggestion he killed him. He says the informer shuttle's engines were sabotaged and that he was left marooned on a planet in the Badlands. Sisko notes that all Eddington did was ensure him a slow death.
Eddington: Can't you see what's happening to you? You're going against everything you claim to believe in. And for what? To satisfy a personal vendetta? Sisko:YOU BETRAYED YOUR UNIFORM! Eddington: And you're betraying yours right now! The sad part is that you don't even realize it. I feel sorry for you, Captain. This obsession with me, look what it's cost you!
Hidden in Plain Sight: Odo realizes this trope is in play when Eddington uses a Breen nursery rhyme as a Maquis signal. The lyrics are irrelevant—what matters is that it's Breen, and therefore a signal to rendezvous at a Breen colony.
Hoist by His Own Petard: Eddington wants to make Cardassian colonies unlivable for them? Then Sisko is going to do the same to every Maquis colony he can find.
Inspector Javert: A comparison brought up numerous times during the episode, due to Sisko's almost obsessive hunt for Eddington. Eddington even starts calling Sisko Javert.
Irony: Starfleet Security assigned Eddington because they didn't trust Odo. After reporting that he found more of Eddington's backdoor viruses in the station computer, Odo makes it a point to Sisko to remind Starfleet Security about it.
It's Personal: Everyone knows Sisko is out for revenge against Eddington. He just doesn't care.
Though initially, Starfleet did reassign the pursuit of Eddington to the starship Malinche because they felt Sisko was too close to the situation. Sisko bucked orders to go after Eddington, then took over the pursuit again when the Malinche was ambushed and knocked out of the fight.
Like You Would Really Do It: Invoked. Sisko threatens to unleash a biogenic on a Maquis colony planet (rendering it uninhabitable for 50 years) and will continue to do so until Eddington surrenders. Eddington doesn't believe "the pride of Starfleet" would do it, but Sisko does. The rest of the crew is similarly surprised.
Oh Crap!: Worf is stunned when Sisko gives the order.
Protagonist-Centered Morality: Let's not mince words here: Sisko commits multiple war crimes in this episode by dropping chemical weapons on a civilian target, and no, the fact that Eddington did it first is not an excuse. And the rest of the Defiant crew is equally culpable for following the orders in question. But the Federation for some bizarre reason lets this slide after Eddington surrenders and simply resettles both sets of displaced colonists on the other's planet.
Repeat to Confirm: Necessary as many of Defiant's systems are hosed by Eddington's virus, including internal coms. As a result, Sisko has Nog relay orders from the Bridge to Engineering, as well as any responses/warnings.
Then Let Me Be Evil: Eddington has a whole Valjean/Javert complex going on with him and Sisko. Sisko eventually realizes that to win, he must stop thinking he's the hero like Javert did.
This Is Unforgivable!: Sisko already had a personal vendetta against Eddington specifically, but he believes the Maquis truly crossed the line by attacking the Malinche.
Villain Has a Point: Eddington directly calls out Sisko for committing war crimes over his personal vendetta; Sisko's only real response is Appeal to Force by threatening to bomb a second planet.