How about they recreate the philadelphia experiment?

...and land in 1947, Antarctica...

No, seriously now. Maybe they're conspiracy-buffs, and decide to recreate 'Project Rainbow'. They wrap the sub in wires, and create magnetic fields that rip them through space-time. They could land pretty much anywhere y'all want.

http://www.abovetopsecret.com/forum/thread171719/pg1
http://www.crystalinks.com/phila.html
http://www.bielek.com/albielek.htm
http://www.history.navy.mil/faqs/faq21-1.htm

EDIT: This ties in with Nikola Tesla's Time Travel Experiments!
http://uforeview.tripod.com/teslatime/teslatimetravel.html

QUOTE
With his experiments in high-voltage electricity and magnetic fields, Tesla discovered that time and space could be breached, or warped, creating a "doorway" that could lead to other time frames. But with this monumental discovery, Tesla also discovered, through personal experience, the very real dangers inherent with time travel.

Tesla's first brush with time travel came in March 1895. A reporter for the New York Herald wrote on March 13 that he came across the inventor in a small café, looking shaken after being hit by 3.5 million volts, "I am afraid," said Tesla, "that you won't find me a pleasant companion tonight. The fact is I was almost killed today. The spark jumped three feet through the air and struck me here on the right shoulder. If my assistant had not turned off the current instantly in might have been the end of me."

Tesla, on contact with the resonating electromagnetic charge, found himself outside his time-frame reference. He reported that he could see the immediate past - present and future, all at once. But he was paralyzed within the electromagnetic field, unable to help himself. His assistant, by turning off the current, released Tesla before any permanent damage was done. A repeat of this very incident would occur years later during the Philadelphia Experiment. Unfortunately, the sailors involved were left outside their time-frame reference for too long with disastrous results...
/QUOTE

nazi submarine in search for the aryan origin?

If the ww2 theme still appeals, the submarine could have been sent out to find the aryan origin (just like special units searched for it in the tibetan montains if i'm right) - namely, atlantis, the sunken city, to find proof for the igeology's foundation of racial surpremacy.

Combine this with Alexander Vervaet's latest idea of encountering a strange form of power.

After those incidents, they could be stranded in some sub-terranean cavity where the lost city lies, presumably deserted. At first they find indications that the mission is a success, should they return, that is, but then finds secrets beyond their ideology which also should pose a threat not only to what they believe in but also to their lives.

real-size sub

nothing storylinerelated, and if the ww2 theme is the way to go, this won't count, but anyway:

We've got a cold-war submarine permanently docked in our harbor. If any submarine movie project is well through-thought enough i'm sure there's a possibility to apply for using it as prop. Not all too many miles away (on the other coast of sweden), there's also an enormous underground facility for reparation of damaged subs (i think the kitchen has ability to serve 3000 persons). It was meant to be the last stand if the cold war would break out. Permission to film there has been granted before, as most of the facility isn't either secret nor in use anymore.

Language of the third reich.

I've got a handy book at home called 'lingua terti imperii' (language of the third reich) which is one of my favourites i always come back to. It was written by a jewish linguist who, because of his expertice, was allowed to stay in germany under restrictions and superveillance. In secret, he wrote a diary where he commented on the changes in the german language which eventually turned out to be the book i've got.

If you need consulting regarding the language and how it formed the thinking in the third reich, i'm all in with all i can offer.

New idea

Since my previous idea seems to be aged I am going to give it another shot:

They are stumbling a bit around at the ocean floor when their scientific equipment (make it a small high tech sub) notice a strange power source, as soon as they enter the power field there are power fluctuations or power spikes (whatever it is, it sounds cool) inside the reactor (if they have one) and they are suddenly teleported to somewhere else. Where they arrive is still a mystery but I am sure someone is going to have a superb idea and post it.

What, more short attention span?!

This is frustrating!

Plot suggestion (but it's not complete)

I've been thinking awhile and I think it's time to rewrite the plot in the line Aaron Agassi suggested.
Setting: somewhere in the future.
Location: Western-Europe

Europe has fallen into poverty and Asia has spotted a new market in the world: the newly upcoming power of Africa.
The Europeans are angered that they, who have meant so much for the world are now put aside and the Governments of the Europe decide unify completely in order to be stronger and before the last funds are gone. In these days the archives of all the governments will be relocated in the European capital (which is still Brussels). It is now the job of a selected team of linguists and professors to sort out the rubbish from the useful documents. A young professor who is recruited because he speaks fluent German finds in the German administration a document which is clearly rubbish but he decides to keep it so he can show it to his small group of students. (Note that the document is written in 1980 by an Eastern-German official, it's directed to Moscow and cites an older series of Nazi-documents about the search of this artifact)
The document speaks about an artifact that has unimaginable powers, not only it brings wealth but it is also a weapon of great value. The students who are still young and thus able to be blinded by fairy tales are very interested in this artifact. They set out on a quest to find the rest of the document, unfortunately they only find what this Eastern-German official said about it, and he states that the submarine transporting this artifact sank for some reason, but the exact location wasn't given only a place where it could be.
After finding enough information the youngsters want to get their own submarine, but don't have the funds to buy one: so they build their own based on the plans of German U-boats they find (the only plans they could get easily) and build their own sub adapted for searching the seas.
And...

'Africa Paradis.' prequil?

I take it that these are fairly high level mechanical engineering students with the wherewithal to duplicate a German u-boat. And for the resources, they must be grad students working with a professor of some sort of corporate sponsored project. But to what end? Forensic archeology? But what don't we really know about u-boats? And don't we still have any preserved and operational u-boats in museums, indeed dating from both world wars? http://www.uboataces.com/articles-uboat-museum.shtml

Does it really need to be a replica u-boat? What if the basic u-boat design was simply repurposed and adapted for anything else, such as ocean research or even just reef site seeing with more glass? Then again, maybe such is just the cover story. Maybe it's a more specific u-boat special prototype, indeed with a great deal of period duplicated heavy glass, that they seek to recreate, for whatever forensic archeology into some or other arcane Nazi research. Then, perhaps in seeking to duplicate whatever lost Nazi expedition, they end up discovering some submerged artifact that summarily discharges a massive electrometric pulse as they approach, and they only survive because their anachronistic sub is not computerized. Only their laptops and cell phones get fried. And perhaps that's what sets back the America! Indeed, I see no reason that 'The Submarine Project' could not be set within the continuity the likes of 'Africa Paradis.' Perhaps licensing could even be obtained as part of a promotional exchange.

But what about conflict? Romantic rivalry? Intrigue and suspense?

Change in paradigm

While they have been gone something have changed?

I am very inspired by this movie-plot: http://www.imdb.com/title/tt0899129/
it is something thought-provoking that africans is not always poor and trying to escape to the north.
Or could an american (submarine) accidentaly destroy some building in a middle-eastern country, that makes that country so mad that they go to United Nations and try to start an invasion of Manhattan. or California...

While a crew travels in a submarine, a long distance, anything, even the power of the world can change, in dramatic ways to create comedy or very serious thoughts for the viewer.

My thoughts are also applicable on a space trip, kind of "planet of the apes"

Base

They also could discovered a secret research facility at the bottom of the sea.