I have a more literal interpretation of the song. It seems to be about climate change, pollution and the destruction of the environment in general. There will be more rainy days in coastal areas when the earth heats up.

“Hey scientist please save us from our rainy day, because your counterpart in in the magic art is manufacturing judgment day”

I believe he’s talking about scientists trying to find a solution for the problems that other scientists who work in industry create in the way of chemicals and other forms of pollution that will lead to our destruction.

“There’s a fell wind blowing out of the east bringing famine drought and plague, well now at least that’s what they say”

I think this line refers to the US always using China as an excuse to not move on reducing carbon emissions. “ They keep opening coal plants so it will do no good if we correct ourselves “

The rain falls like judgment because it is our fault the earth is warming.

“ When a man gets down on his knees to pray, you know he’ll find what he is able. Chances are he’ll find it either way “

Destruction of the environment is what will drive humans to extinction, praying is the metaphor for the desperation when it happens. Chances are we’ll go extinct anyhow.

“ Oh lord have mercy on a humble man,lost in the wilderness without a guiding hand”

The average Joe who doesn’t know any better and has no political leaders that care to try and fix it

The beginning is akin to previous statements of 'trying to maintain objectivity' between the claims of science and [s]JK Rowling[/s] religion. They use their usual trope of making a demand of a certain type or role of person, in order to illustrate their deficiencies in some way, as in 'I Want to Conquer the World.' In a song notably about the various meanings of 'rain,' metaphorically and so on, saving someone from 'rainy days' is a humorous drawing on the multiple meanings of the phrase, and in a sense expresses a certain sense of limitation in the general ethical neutrality of science, akin to that which Marx criticised in political economy, although in this case less explicitly critical and more in the form of a generic sense of lack. It is hence a portrayal of a sort of search for meaning among the dual barren lands of science and religion.

Hence, for instance, they are quite able to switch into an explicitly religious framework, as with, 'Oh lord, have mercy on a humble man / Lost in the wilderness without a guiding hand.' While it's still ambiguous, nonetheless there is a sense of not really clinging too strongly too either side, due to still feeling slightly 'lost,' which hence causes them to call upon God. The 'wilderness' is, of course, also a religious term, as with the Israelites or Jesus, and in general lacking a guiding hand there might be compared to the situation of Jesus, for instance. Because the song is ultimately not that resolved about science and religion, aching in a sense for the pathos of religion, and just generally expressing a sense of being lost, there is a lot of elision when they're brought up explicitly.

The second verse comes across as a bit of an inadvertent parody of Hamlet. Nonetheless, 'I know that evil exists,' is a more certain statement than you'll find in most Bad Religion songs, and in that sense they're looking for something which can firmly anchor such a sense, and also connect it to their everyday life, which in general can tell them where to look rather than just that they should pray for - something or the other.

The speaker is hence generally speaking to be portrayed as 'agnostic,' and hence they are quite willing to [s]eclipse Taylor Swift in every way[/s] draw on religious terminology or only vaguely qualify religious claims. In general, it deals with a search for something decisive, which they would appreciate, and which anchors the pathos of the song, but at the same time the sense of meaninglessness which they are plunged into elsewhere, and hence can be summarised as an unresolved search.

To me, this is largely self-explanatory and keeping with the rich, recurring theme of Bad Religion. My interpretation is that this is heavy, heavy guitar, heavy lyrics, fucking amazing song. Simple but unique.

I do wonder about the the fell wind blowing out of the East? Is that a reference to Islam, perhaps?

Is it only me or this whole song is a reference to the story of the Noah's ark?

My interpretation without parsing this awesome song line to line and verse to verse is an overall message of caution to not be apocalyptic about any sort of disaster or tragedy yet don't expect science to explain everything. Science will always be incomplete regardless of how definitive that specific discipline can explain events. It addresses the feud amongst naturalists and creationists that has always been waged on an impasse. No one can claim an answer to the unanswerable. Whether it be a grand design by a deity or the havoc the cosmos can wage, It is a "non-issue" that is futile to explore.

"Hey, scientist please save us from our rainy days
Because your counterpart in the magic art is manufacturing judgment day"

I think this an ironic statement, done positioning the singer in the voice of a non believer, who asks what he knows is true (science) to save him from the Rainy days, which represent the supposed punishment from God. Now the argument of the song is that the counterpart of science (i would assume this means all Religions) is deliberately inventing the story of judgement day. This may be further established when the song says:

"There's a fell wind blowing out of the east
Bringing famine drought and plague
Well now at least that's what they say"

Especially the last part, meaning that judgement day (and maybe by extension everything that Religion proclaims) is an invention.

The importan part of the second verse, i think is this:

"When a man gets down on his knees to pray you know he'll find what he is able
But chances are he'll find it either way"

Accentuating the fact that we don´t need to be fearfull of some supreme force, or appeal to it, to be able to go on about our lives.

Then the chorus summarizes all:

"Rain fell like judgment
Across my windowpane
Said it fell like judgment
But it was only rain"

I interpret it like this:
From inside our homes (or lives) watching from our windowpane into the whole Religious movement and the terrible things that happened in god´s name, some may start to be decieved, and not see the actual reality. That even though it fell like Judgement, it was Only Rain.

I am somewhere along the lines of the rest of you- it's about humanity's unfortunate disposition to assume "supernatural forces" or "fate" or other such things are responsible or lifes many ups & downs. The metaphor here being similar to one of the oldest supernatural rituals- a "rain dance" may have come as a "signal from God" of approval or something similar but....in reality....it's Only Rain....nothing more.

Mickey, that is exactly similar to my interpretation; only with the help of science we are able to reveal that things don't happen because of supernatural forces. So in the past lightning was thought of as a sign from the gods, but today we know it happens because of electronic charges in the atmosphere. Same with the rain in the song wich is interpreted by "the counterpart of science" (supernatural or religious believes) as a sign of god as judgement for the sins of the unbelievers in the east (secular europe or islam) but in the end it's just rain.

People attribute bad things to some sort of religious (magic) punishment, but in reality the explanation is much simpler. In this case, it's only rain -- not God's judgment.

I imagine a former soldier being back home not sure whether he has done the right thing.

"Rain" = sound of gunfire
"Counterpart to scientist" = religiously motivated warrior
"East wind" = Taliban & friends
"They" = Bush, Blair & friends

I think that this song, since it was written by Brett, must have something to do with his acceptance of his past and asking for the people in his life to forgive him for his actions of his past.