As promised, I just watched the relevant scenes in Crimson Tide. Here’s what happens:
First, sonar detects an unknown sub. They dive & turn away to evade.
While they’re diving, they get the EAM that the Russian rebels are fueling their missiles, and that they are to launch 10 missiles at them. They do all the confirmation with 4 officers that the orders are authentic, and tell Weapons Officer Aragorn (son of Arathorn) to set SQ1. It will take 14 minutes to prepare to launch.
They’re still diving. As they pass 550 ft, the radio room reports that VLF contact is lost. Captain orders that they extend the ELF antenna. They play this as pretty standard procedure, Denzel isn’t involved at all.
Sonar reports that the sub is an Akula. Previous exposition has indicated the rebels have 4 Akulas.
Radio starts receiving an EAM on ELF, but they’re too deep to receive the message. Denzel asks Gene to go shallower to receive it, Gene won’t - says with the Akula around, it’s too dangerous. He’s going to wait till the missiles are ready, go up to launch depth, and launch. Denzel requests that they float the radio buoy, Gene says OK. So at this point, the squabble is still very minor - an officer suggests one course of action, his superior decides on something else, he makes another suggestion that is accepted. Though this wasn’t in the dialog, here’s one way to read it:
Denzel: We know from the ELF they’re trying to send us another EAM. We should move shallower to receive it.
Gene: Too dangerous. We’ll go up to launch depth when we’re ready. If we get another EAM there, we’ll deal with it then.
Denzel: Then we should extend the buoy. If we do get another EAM cancelling the launch, we won’t have to come to launch depth at all, which decreases the chances the Akula will find us.
Gene: OK.
Again - that’s not in the movie, but those are the motivations I read into the scene.
They start to extend the buoy, the winch jams, makes lots of sound. The Akula finds them, fires 2 torpedoes. While the torpedoes are in the water, another EAM starts to come in over the buoy. Both torps miss, but one explodes fairly close and breaks the buoy cable, and somehow breaks all the radios as well (all other damage at this point is very light). From this point to the end of the movie, all the radios are broken. Denzel goes to Gene with the interrupted message, Gene doesn’t give a shit, Denzel refuses to concur on any more orders to launch missiles until they can find out what the interrupted EAM was, big shouting match, COB sides with Denzel because the Capt. can’t relieve the XO for refusing to concur, Gene gets confined to quarters.
Denzel starts back up to periscope depth, Akula finds them, another fight, they kill Akula but Akula almost kills them, lots more damage, Lt. Tony Soprano organizes the other officers to get the Capt out of arrest, lots of running back and forth between armed sailors on each side. Finally at the end they fix the radio and find out the launch is cancelled.
So I’d say apart from the first near miss doing no damage except breaking every radio on the boat, the internal movie logic through this sequence is pretty consistent. It’s basis in reality has already been addressed by robby above.