The story's central irony is that the Martians are so strong (in terms of weapons and technology) but ultimately so weak against basic bacteria on earth. In Book 2, Chapter 8, the narrator emphasizes the strangeness of this situational irony:
A mighty space it was, with gigantic machines here and there within it[...]scattered about it, some in their overturned war-machines, some in the now rigid handling-machines, and a dozen of them stark and silent and laid in a row, were the Martians – dead! – slain by the putrefactive and disease bacteria against which their systems were unprepared; slain as the red weed was being slain; slain, after all man’s devices had failed, by the humblest things that God, in his wisdom, has put upon this earth.
In this passage, the narrator highlights the irony of the Martians' death by bacteria by calling that bacteria one of the "humblest things that God [...] put upon this earth." In contrast to the Martians' fancy technology, the bacteria seems very weak and harmless. But the same technological advancements that allowed the aliens to invade earth also permitted the complete elimination of earthly bacteria from Mars, which left the Martians vulnerable upon arrival. The irony, then, is that the very qualities that enabled the Martians to prosper are also the qualities that eventually lead to their downfall on earth.
