Irony of Ares's Plan
Ares has been launching catastrophes against the human race in an attempt to forge a human's will strong enough to resist being "assimilated" into the Serpentine Army, thus destroying it from the inside like a virus. This plan fits into his philosophy that in order to build a great new world, you must destroy the old one. Ironically, his plan turns out to be entirely pointless; David Vale is the one who resists the assimilation and destroys the serpent, a man Ares hates and tries to kill on multiple occasions.
Irony of the Divorced Couple
Mary and Paul are divorced, and they haven't spoken in years. Ironically, when she discovers a signal of extraterrestrial life, Mary has to call Paul because of his experience and position, and they have to work together to save the human race. An unlikely yet amusing coincidence.
Irony of Resurrection Syndrome
The resurrection tubes have the ability to bring dead people back to life exactly as they were prior to their death, only with perfectly healthy bodies. Ironically, this resurrection is sometimes detrimental: when the person experienced a traumatic death or memories that make them unable to cope with life, they are often resurrected with fatal illnesses. This ironic disease is termed "resurrection syndrome."
Irony of the Serpentine Army
The Serpentine Army is an enormous, incredibly powerful entity made up of powerful ships and the collective minds of thousands of intelligent beings. Its power is unrivaled, and it would have had the ability to destroy Atlantis without any trouble whatsoever. Ironically, this monstrously powerful entity is destroyed by a single man who simply refuses to be integrated into the machine. This human's (David's) DNA acts like a virus, and the serpent collapses from the disease.
Irony of Extraterrestrial Communication
When Mary receives the signal that signifies intelligent extraterrestrial life, she is overwhelmingly excited. The ironic truth of this communication, though, is that is could either be great news or terrible news, and it's impossible to determine this from a single message. It turns out to be terrible news (the Serpentine Army), which makes the initial joyous reaction ironic.
