Is it correct ?
"He was afraid that his friend couldn't be on time to board the plane so he called to make a fake bomb scare."

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You need a subjunctive here, so it should be 'wouldn't be' not 'couldn't be'.

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"Because he was afraid that his friend couldn't be on time to board the plane, he called to make a fake bomb scare."

I would separate the sentence into a conditional (separated by the comma ",") just so it flows better.

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He was afraid of that his friend couldn't be on time to board the plane so he called to make a fake bomb denouncement.

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Thank you Nathalie

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It's very good, I would just write it as follows: "He was afraid his friend wouldn't board the plane on time so he called to make a fake bomb scare."