Submitting a manuscript that is not ready yet just to fulfil a contract I am part (working part time) of a research project that is funded by the government in another European country (not the one I live in). As part of my contract with that project, I'm required to submit a manuscript reporting the research to a peer-reviewed journal by a deadline. 

However, because of unforeseen circumstances (mainly related to methods that didn't work as expected), the manuscript was not ready for submission by the deadline. In fact, it received very critical responses when presented at a conference earlier this year, and it is clear that major changes have to be done before it is ready to submit. That conference is organised by the same association that publishes the two journals that I had in mind when writing the paper, so I think that I should heed their advice. 

Yet, I'm being forced to submit it by the deadline or I will face a fine. My co-author, who is from that other country, has been very clear that I have to submit the article, period. That co-author has been very helpful in buying me time, but the changes needed are very time demanding (I need to basically re-do the whole study), and I'm not working full time on that project.

What is the most sensible thing to do? Can I just submit it anyway? I thought about sending it to a journal where I expect it to be desk-rejected just to fulfill my contract, and then do the necessary changes to submit to the journal I originally intended to send it to. Would it be ethical? What other options do I have?
Contracts for scientific research can often be thought of as having two components:


A set of "minimum requirement" fixed deliverables that you must accomplish or else face penalties, and
A set of actual goals, which may or may not be able to be accomplished as anticipated, given the uncertainties of every sort of interesting research.


Typically, the fixed deliverables are things like "write annual reports" and "create a prototype implementation of X" that should be able to be accomplished as long as the research is progressing well.  

"Submit a paper on this research," on the other hand, is a foolish requirement to have in a contract, because whether a paper should be submitted at a particular time or not is very dependent on context.  For example, you might have been doing wonderfully, but then be unable to submit as anticipated because of related work that other people have published in the mean time.  It is for this reason that in my contracts I typically propose something more vague like, "communicate with scientific community on results of the research" and put the fixed deliverable as reports to the funder on what we've done.

So something's already rather screwy in your contract, and you need to deal with it.  I think the most important thing to figure out is whether the pressure to fulfill the letter of the contract is coming from a program manager who cares about the research or an accountant who does not.  Talk to the leaders of the project and see if they can figure out, because my recommended path depends on which it is:


If the pressure to publish comes from an accountant or similar "box-ticking" authority who does not actually care about the research, only about fulfilling the ridiculous contract, then I would recommend fulfilling the technicality by asking something like Nature or Science to desk-reject your manuscript.  Confirm the plan with your co-authors and others on the team, and make it clear what you are doing in your cover letter, and I'm certain they will provide you the rejection you desire without doing any significant damage to your career.
If the pressure to publish comes from a program manager who actually cares about the research, then you are in a much more difficult situation, and the desk rejection ploy is unlikely to satisfy them.  At the same time, the program manager could likely grant an exception to the contract to allow you to not submit. In this case, I think that it is important to understand why there is so much pressure to submit (perhaps it signifies that the whole project or program is in trouble?), and for the project leaders to negotiate with the program manager.  If they've already done so and failed... well, you're stuck in a bad situation.


If you're in the second situation, negotiations have failed, and you really must submit, I would recommend not submitting results that you believe should not be published.  That is the sort of thing that can haunt you for your career.  Instead, I would recommend submitting the part that you are comfortable with---the study design---in a paper that clearly and honestly says this is all that is done right now and puts the completion of the new study into future work.  Make sure that anything you submit is something that you would actually be OK with seeing in print if it does get through the peer review process, and make it clear in your cover letter that you are aware that this is preliminary and will be happy to accept a decision by the editors to either proceed or not.

And then never accept a contract with such a horrible clause in the future.