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> 東京は今雨が降っている。

**literally:** Tokyo now rain is falling.

Question: why Tokyo is [wa]-ed but not [ni]-ed?  
Is it allowed to say the same idea in English manner like this?

> 東京に今雨は降っている。  
>  東京では今雨は降っている。

**literally:** In Tokyo now rain is falling.

Or maybe rain always must be with [ga] and never with [wa]?

To my mind I thought that what is marked as [wa] is the acting object of the
verb at the end of sentence. If here verb is [to fall], then to my mind
[wa]-ed Tokyo must be falling.

Or maybe the key to this situation is that the real verb here is not 降る, but
maybe the real verb in this sentence is 雨が降る? And therefore 雨が never should be
separated from 降る and they should stand always together like "husband and
wife"?
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particles particle-に particle-は phrases particle-が
Rain in the city
> Or maybe rain always must be with [ga] and never with [wa]?

If you want to simply say "it's raining", you have to use が. But you can use
雨は in the following situations:

  * You really want a contrastive meaning, e.g. 雨は降っているが雪は降っていない.
  * You refer to a certain rainfall episode that has been already brought into the universe of discourse, e.g., 雨は止んでいます (" _The_ rain has stopped").

From here, let's just use が and compare these sentences:

  1. 東京 **は** 雨が降っている。
  2. 東京 **に** 雨が降っている。
  3. 東京 **には** 雨が降っている。
  4. 東京 **で** 雨が降っている。
  5. 東京 **では** 雨が降っている。

There sentences are all correct. The _subject_ is 雨, not 東京. 東京 is a _topic_
when there is は (1, 3, 5). Here, I think に is a direction/destination marker
rather than a location marker which can be used with いる/ある/etc (i.e., rain is
falling _towards_ the land of Tokyo). で is a location marker that marks the
place where an action takes place. は is a topic marker, which can [directly
follow に, で, から, etc](https://japanese.stackexchange.com/a/17574/5010).

には can often be "contracted" to は. For example you can say both 誕生日はパーティをします,
誕生日にはパーティーをします and 誕生日にパーティーをします, but when there is は, 誕生日 is topicalized.

Related:

  * [What is the difference between "に" and "には"?](https://japanese.stackexchange.com/q/1096/5010)
  * [What's the difference between には and では](https://japanese.stackexchange.com/q/9391/5010)
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answer
While I'm not able to pin down your focus in the question, I guess you're
having trouble understanding the function of は, in grammar and in mental
model. You may have already heard about that は marks _topic_ , which is not on
the same level with _subject_ , _verb_ (predicate), or _object_. What does it
actually mean?

Think of a theater, where actors play as they like on the stage. Interactions
between actors can be described as sentences using grammatical relations like
_subject_ and _object_. When you say English sentences require a _subject_ ,
it means that you can't make a sentence until you mention at least one actor.
By the way, actors can't perform in the middle of nothing. They can't fight in
the void like gods before the world creation. There have to be an implicit
scene, a backdrop, a stage. A Japanese sentence requires a _topic_ , that
means, you must set up a scenery before you talk about who did what. What
becomes _topic_ is marked by は.

Of course, は is not always detached from actors. You can take out one of them
and put the one as a background, like a king on the throne in the middle of
the stage but does nothing, just signifying they're in the palace now. That
makes an element is a topic and a participant at the same time. Such things
are marked by appropriate particle + は: には, では, とは, からは etc. Note that が (≈
subject) and を (≈ object) are eaten by は, so when you see a bare は, you must
suspect three possibilities: が + は, を + は, and the isolate は.

So,

> _**literally:** Tokyo now rain is falling._

No, it's like "Tokyo​ **:** now rain is falling."

> 東京に今雨は降っている。

This is a grammatical sentence but not the most natural one. に used in this
manner is archaic or poetic, not in the regular language. は put in the middle
of sentence could have various special connotations, such as saying "not
snowing but raining" or "raining it is".

> 東京では今雨は降っている。

The default interpretation of this sentence is, I guess, "It is indeed raining
in Tokyo".

If I'd like to tell the meaning in the English-compatible way, I'd say:

> 東京では今雨が降っている。
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