The irony of the mark
Without her permission or control, Fiona realizes that the mark on her hand, which she hid with concealer out of habit, is actually a mark of doom on her. This death mark is a picture not of her worthlessness or the meaninglessness of her life; it's a mark (which is a symbol with meaning), implying that although this novel explores the brevity of life, it does so from the position of meaning. Fiona's life means something, and she knows it. But does it make her special? Is it because of her individual value that the mark is meaningful? No, it is because she is human.
The irony of guns and law
The novel shows that guns are a kind of power, and in the frayed, decomposing future of apocalypse (that the novel predicts fictitiously), the guns are a new, ironic kind of law. Although the laws of society are designed to prevent unbridled violence, they have to remain powerful to accomplish that. In the anarchy of Fiona's nightmarish life, guns are law.
The irony of Bowen
To find a classmate in the apocalypse is a grand irony, and so is Fiona's response to him. Even though it makes no sense for her to try and make a family when she is so close to the end of her own life, the urge arises of its own accord. This irony is a pointer that, no matter how bad life gets, Fiona still assumes naturally that if she can survive the immediate threats of her environment, she would still want to be in a family when all is said and done. It's ironic that she should care about these things at such a time.
The irony of Arrin and Fiona
Arrin explains to Fiona what dramatic irony she still doesn't know about. That means Arrin is a kind of Prometheus character, exposing the secret order to Fiona. In Arrin's ironic instruction, Fiona's normal expectations are reversed. If people find out she is a woman, she will be abused and regarded as property. If she gets caught by the forces that be, she will be ironically greeted not with social order but by extreme disorder.
The irony of the ending
If Arrin agrees to kill Fiona, she can spare her life, maybe. There is the chance that it is just a trick, that they will secretly kill both, and they are just allowing Arrin a chance to do something treasonous and horrible before her death. It's ironic for this, and because Fiona is the one person it would be hardest for Arrin to kill. She loves Fiona because she has vested interest in her success.
