When Tom Cruise sees birds on the alien ship at the end of War of the Worlds, he told the major.
But how/when was the armor of the alien ships removed? That was not described properly.
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The "armor" (force fields) of the alien vessels failed after the alien crew inside died from exposure to Earth microbes, which is also how the invasion as a whole was brought to a crippling halt. The idea was that the alien immune systems had no defense against Earth-born viruses, as they had never been exposed to these illnesses before, and so something that would only make a human mildly sick turned out to be deadly to the aliens.
This is the sort of thing that has historically been a very real threat for colonists arriving on a newly discovered continent here on Earth, so it made sense as a science fiction story ending at the time the book was originally written.
The realism of this ending has been called into question more recently, as some people have observed that a virus which can have severe effects on human health will often have little or no effect on other Earth mammals. If a given virus isn't even able to universally infect (no pun intended) all species on this planet, what are the odds one would have any effect at all on a completely alien biology?
Although cross-species transmission is rare here on Earth, those viruses that DO make "the jump" often end up having far more serious consequences in the newly infected species. Memorable recent examples include SARS and the bird flu.
My personal opinion is that it's possible (though very unlikely) that an Earth-born virus might manage to infect the alien population, and having done so, it would almost certainly be fatal. It's close enough that I'm willing to suspend my disbelief, anyway. Also, the extremely low probability of such a transfer would help to explain why the aliens weren't prepared for it (you would think a highly advanced alien race with technology far surpassing our own would have thought to wear hazmat suits during the invasion, unless they had reason to think it wasn't necessary.)