Can this sentence be rephrased as "I will come back after two minutes"?
I will come back in two minutes.
What's the difference between in and after in this context?
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In is the normal preposition when the reference frame is the current time.
Stay here and wait for me. I am going out and I will come back in two minutes.
Using after isn't really wrong but doesn't feel idiomatic. With after, I get the impression that the elapsed interval is important, rather than the moment in time when the action happens.
I am starting the engine, and I will switch it off after two minutes.
After conveys that what determines the switch-off time is that the engine should run for two minutes. Contrast with
I am starting the engine, and I will switch it off when he comes back, in two minutes.
If the reference frame is not the current time, then in cannot be used. The idiomatic way to express a time interval uses the adverb later.
When the bell rings, I will go out, and I will come back two minutes later.
(“I will come back in two minutes” would mean that the speaker will come back two minutes after saying this, irregardless of when the bell rings.)
It is also possible to use after, and that feels a bit more idiomatic than when the main clause is in the present tense. As before, after emphasizes that it is the elapsed interval that matters.
When the bell rings, I will go out, and I will come back after two minutes. This should give you time to come to a decision.