hon wo yonda ato, hondana ni simaimasu.

Because あと means after, and when a verb comes before あと, Japanese usually uses:

• verb in plain past form + あと

So:

• 読んだあと = after reading

This does not mean the whole sentence is in the past. It just shows that the reading happens first, and the next action happens after that.

Compare:

• 食べたあと = after eating
• 見たあと = after seeing
• 帰ったあと = after going home

This is a very common pattern in Japanese.

Because the two verbs are doing different jobs.

• 読んだ is inside the time expression 読んだあと = after reading
• しまいます is the main verb of the sentence

So the sentence structure is basically:

• [After reading the book], [I put it away on the bookshelf].

The tense of the main action is shown by しまいます.

• しまいます = non-past polite
• しまいました = past polite

That means this sentence could describe:

• a habitual action: I put it away on the bookshelf after reading it
• a future action: I’ll put it away on the bookshelf after reading it

Context tells you which one is meant.

を marks the direct object of the verb.

Here, the verb is 読んだ from 読む (to read), so:

• 本を読む = to read a book

In this sentence, 本 is the thing being read, so it takes を.

Even though 本 appears near しまいます, it belongs grammatically with 読んだ:

• 本を読んだあと = after reading the book

Here に marks the destination or place where something is put.

• 本棚にしまいます = put it away in/on the bookshelf

With verbs of placement like 置く, 入れる, しまう, に often marks the location the object goes to.

Examples:

• 箱に入れる = put it into a box
• 机の上に置く = put it on the desk
• 本棚にしまう = put it away on the bookshelf

So に is not marking the object. It is marking the target location.

Here しまいます is the polite form of the verb しまう, meaning:

• to put away
• to store
• to put something back where it belongs

So in this sentence, it means physically putting the book back onto the bookshelf.

This is different from the grammar pattern 〜てしまう, which can mean:

• doing something completely
• doing something unfortunately/regretfully

That is not what is happening here.

This sentence uses the independent verb:

• 本棚にしまう = put it away on the bookshelf

Yes. The reading is:

• 本 = ほん
• 棚 = たな
• 本棚 = ほんだな

This is a common sound change in compounds. Even though 棚 by itself is たな, in 本棚 it becomes だな.

Other readings in the sentence are:

• 読んだ = よんだ
• あと = あと
• しまいます = しまいます

Because Japanese often leaves out the subject when it is clear from context.

So instead of saying:

• 私は本を読んだあと、本棚にしまいます。

Japanese can simply say:

• 本を読んだあと、本棚にしまいます。

The listener usually understands who is doing the action from the situation.

This is very normal in Japanese. In English, you usually need a subject, but in Japanese it is often omitted.

あと means after.

When attached to a verb phrase, it creates a time expression:

• 本を読んだあと = after reading the book

This whole part tells you when the main action happens.

So the sentence structure is:

• time expression
  • main action

In other words:

• After reading the book, ...
• ... put it away on the bookshelf.

Yes.

The ending しまいます is in the polite non-past form, and Japanese non-past can express both:

• future actions
• habitual/repeated actions

So depending on context, it could mean either:

• I will put it away on the bookshelf after reading it
• I put it away on the bookshelf after reading it

If you were telling someone about your usual routine, this would naturally sound habitual.

The comma is there because 本を読んだあと is a long introductory time phrase.

So the comma helps separate:

• after reading the book
  from
• put it away on the bookshelf

It is similar to English writing:

• After reading the book, I put it away on the bookshelf.

In Japanese, commas are often flexible, so the sentence could sometimes be written without one, but using it here makes the sentence easier to read.

Yes.

You can say:

• 本を読んだあと、本棚にしまいます。
• 本を読んだあとに、本棚にしまいます。

Both are natural.

The に after あと makes the time relationship a little more explicit, but in many cases it is optional. The version without に is very common and sounds perfectly natural.

In normal interpretation, yes.

Even though Japanese does not repeat the object in the second part, the natural understanding is:

• After reading the book, [I] put it away on the bookshelf.

Japanese often leaves out repeated information when it is obvious.

So the unstated object of しまいます is understood from context as the same 本 mentioned earlier.