Act Twelve: Wait, we won? Dang!
Location: Lab of Evil.

DQ3: Why?
Dr Old: How many reasons. Reasons. Not enough time, to explain.
DQ3: After all this time!
Dr Old: Stop! Wasting! Your life!
DQ3: I don't know how I'm going to get us all out of here.

Dr Old gives DQ3 a key.

Dr Old: I been twenty years. Under the oceans. I make discoveries. Will be lost, lost to the rest of the world! S'why I brought you, son.

Well, I'll be knockwursted! It was his dad all the time! DQ2! Though I'm pretty sure you'd recognise your own father even after twenty years. Anyhoo.

But also, 'that's why I brought you'? How did he bring him? It seems there was at some point a subplot whereby DQ2 is attempting to end the 'Dark Waters' program by the, odd, methodology of having his son and his former colleague arrive on the submarine, and, presumably, merely by their presence, make it all go away. This is irritating for two reasons,
A: After you've removed a subplot it's common courtesy to have a quick flick through the script and make sure you've got all of the relevant dialogue expunged.
B: A subplot that eliminates most of the 'coincidence' plot hooks is a good thing.

Cut to: Flash back, and DQ2 wasn't dragged off after all, he walked off with some people!

DQ3 nods and wanders off.

Cut to: Mikos and Robin near the filing cabinets.

Mikos: We gotta get out of here!
Robin: Who was that?
DQ3: He was, uh, a friend of my fathers.

DQ3 puts the key in a thingy.

Robin: What are you doing?!
Miklos: We don't have time! We got one shot to escape on the minisub!
DQ3: Look look look, we might get only a thousand yards before they release the sharks on us, OK?

DQ3 starts tapping on the weirdly blank keyboard, and starts the auto-destruct sequence.

Yes, that's right folks, the guy uses a key, and taps a few keys and somehow has the authority to blow the fucking lab up.
Incidently, the list of available commands are;
Regulate the Metabolism of Lactose in Cells - Lactose is presnt in mammalian milk, so presumably this refers to the staff, not the sharks.
Regulate the Cell Cycle - Which means, well, nothing, really.
Blastualtion - This is the process where embryonic cells become blastules, so, an early stage of cell deviation. As all the sharks are fully grown, this is presumably irrelevant.
Neuralation - This is probably meant to be neurulation, the stage of cell deviation that results in neural cells.
Gastrulation - This is another early stage of cell deviation.
Embryonic Induction - Er, this would have to mean 'making it become an embryo'.
Oxygen level Change - Self explanatory.
Homeotic Gene Regulation - These refer to the genes that control the formation of different kinds of cells.

In essence all of the commands cover the earliest possible stages of basic cellular growth of a foetus except for the self destruct.

Cut to: the control room

Captain: Foster, come in Foster!
Commander Chap: Sir! We have to shut down the containment now!
Captain: It was activated by the Doctor, get Doctor Combs up here now!

Funny, isn't it, how he only refers to DQ2 as 'the Doctor' but he calls the other one 'Doctor Combs'. Obviously that is handy as calling him Dr Quatrell all through the film might be a bit of a giveaway.

Commander Chap: Doctor Combs to the bridge! Doctor Combs to the bridge now!

Cut to: The evil lab.

DQ3: Get those valves to open the hatch now.
Miklos: Got it!
Robin: Damnit, I knew this sub was familiar! This sub was built on the hull of a Trident!

Trident is a missile system. In the United Kingdom submarines that carry trident missiles are sometimes referred to as tridents, but not in the US. This would be an Ohio class boat, colloquially known as 'boomers'.

Mikos: So?
Robin: So you lose the shark tanks and lab and this is a normal sub, everything except this door.

Well, except for that door, the minisubs, the corridors, the marine contingent, the command staff being the three stooges, the brig and the staterooms, maybe.

Miklos: Guess they taught you something at MIT before they kicked you out, huh?

The Massachusetts Institute of Technology does courses in the intricate details of intercontinental ballistic nuclear missile submarines? Cool.

Robin: Yeah, enough to know you don't put screen doors in a submarine.
Miklos: What?
Robin: Old Polish joke.

Act Eleven: The Battle of the Catwalks

Act Thirteen: Bomb? What bomb?