When a man whose jobs is to take on identities suffers a malfunction with his new one, the man struggles with his identity vs the identity is suppose to be under, which could reveal the status and whereabouts of a new complicated nuclear sub.

A man is implanted with the memories of a person that can identify the location of a submarine but he is now swapping between his own and the implanted memories causing an identity crisis and endangering the mission.

Very wordy. ?I'll get back after some more work.

What malfunction does he suffer? That is very vague.
As a result, I have no idea what your story is actually about.
I'll try to create a logline, but obviously, yours will be different.
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When a nuclear sub goes missing, an undercover agent must (Impersonate a powerful weapons buyer) to discover its location, but complications?arise when (he falls for his mark and accidentally reveals his true identity)
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So if the leads job is to recover the missing submarine. Then the inciting incident would be when the sub goes missing...?(When a nuclear sub goes missing)

...Suffers a malfunction with his new one, the man struggles?with his identity vs the identity?he is supposed to be under.??but complications?arise when (he falls for his mark and accidentally reveals his true identity)
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So his job is to find the sub but he suffers a malfunction because he falls for his mark. The malfunction?being; he reveals his true identity.
Now Malfunction isn't vague, we know exactly what that malfunction is and know what the story is about.