अगर ट्रेन में देर है, तो हम स्टेशन पर इंतज़ार करेंगे।

They form an if ... then ... pattern:

• अगर = if
• तो = then

So:

• अगर ट्रेन में देर है = if the train is delayed / if the train is late
• तो हम स्टेशन पर इंतज़ार करेंगे = then we will wait at the station

Hindi often uses this pair to make the logic of the sentence very clear.

Not always. Hindi speakers often drop तो if the meaning is already clear.

So all of these can work:

• अगर ट्रेन में देर है, तो हम स्टेशन पर इंतज़ार करेंगे।
• अगर ट्रेन में देर है, हम स्टेशन पर इंतज़ार करेंगे।
• ट्रेन में देर है तो हम स्टेशन पर इंतज़ार करेंगे।

Using अगर ... तो just sounds especially neat and explicit, which is why learners often see it first.

Because Hindi commonly expresses this idea with देर:

• देर = delay / lateness
• देर है = there is a delay / it is late

So ट्रेन में देर है literally feels more like there is delay with the train than the train is late, even though the natural English meaning is basically the same.

This is a very common Hindi way of speaking. You may also hear more colloquial alternatives such as:

• ट्रेन लेट है = the train is late
• ट्रेन देर से है = the train is running late

In ट्रेन में देर है, में is part of an idiomatic pattern: X में देर है.

It does not translate word-for-word as English in in a very literal way. Instead, it marks the thing or situation in which the delay exists.

You can think of it like:

• काम में देर है = there is delay in the work
• ट्रेन में देर है = there is delay with the train

So this is something to learn as a phrase, not by trying to match English prepositions exactly.

Because पर usually means at/on, and स्टेशन पर is the normal way to say at the station.

• स्टेशन पर = at the station
• स्टेशन में = in the station / inside the station

If you are just talking about the general location where you will wait, पर is the natural choice.
If you specifically wanted to emphasize being inside the station building, में could make sense.

इंतज़ार is a noun meaning waiting or expectant waiting, and Hindi commonly combines such nouns with करना (to do) to make verbs.

So:

• इंतज़ार करना = to wait

Then करेंगे is the future form of करना here, so:

• इंतज़ार करेंगे = will wait

This noun + करना pattern is extremely common in Hindi. For example:

• काम करना = to work / to do work
• सफ़र करना = to travel
• कोशिश करना = to try

Because it matches the subject हम (we).

Here:

• हम = we
• करेंगे = will do / will wait (plural form here)

So the full second clause is:

• हम स्टेशन पर इंतज़ार करेंगे = we will wait at the station

If the subject changed, the verb form could change too. For example:

• मैं ... करूँगा / करूँगी = I will do
• वह ... करेगा / करेगी = he/she will do

This is normal in Hindi.

In conditions, Hindi often uses the present form in the if clause even when the overall meaning is future:

• अगर ट्रेन में देर है, तो ... = if the train is late, then ...

This is actually similar to English, which also says:

• If the train is late, we will wait

So Hindi does not need a future form in the first clause here.

Hindi is generally Subject-Object-Verb, and the main verb usually comes at the end of its clause.

A rough breakdown is:

• अगर = if
• ट्रेन में = with/in the train
• देर है = there is delay / is late
• तो = then
• हम = we
• स्टेशन पर = at the station
• इंतज़ार करेंगे = will wait

So the important thing to notice is that the final verb phrase इंतज़ार करेंगे comes at the end.

Yes, very often.

Hindi frequently drops subject pronouns when they are understood from context. So this is also natural:

• अगर ट्रेन में देर है, तो स्टेशन पर इंतज़ार करेंगे।

That still means If the train is delayed, we will wait at the station, assuming we is clear from context.

Including हम just makes the subject explicit.