I tried to sleep and get some relief from my troubles, but I cold sleep only a little bit.
I believe the thesis has an interesting introduction and some good dissertations about the data.
But if my psycological feeling do not changes I wouldn't be able to finish the thesis in time

It is completely understandable that you having trouble sleeping. This is a horrible and stressful situation.

If you can write your thesis, without any of the faked data and have a good explanation for why you your papers have additional analyses not in your thesis, this may be a good option (as others have said)

Other people suggested you say the papers were joint work ( you and your supervisor contributed) and you didn't include your supervisors contributions in your thesis because they weren't your own work.

maybe even put in a footnote at the end of those chapters saying something to the effect of ' a version of this chapter was published in X journal, with additional analyses conducted by by supervisor and co-author Dr.Y''

This seems like a good way of publicly distancing yourself from these results.... but maybe it is making to big a point about it... I would be interested in hearing what other people on the forum think about this idea.

I think you should also seek some counselling, just to deal with the stress...there a lot of psychologists , who have also done phd's as part of their training (not all have, in my country phd and clin psyc are different training, but in other countries you do a research phd first), so they may be able to understand what your going through and maybe even offer some advice.

Yep I agree, I would be doing option 3 of my original suggestions if I was in your position.

Remember what happened to the stem cell person who faked data. She looked like a scapegoat to me.

Don't use any of the fake data in your thesis, that is just asking for trouble and you would be complicit in fabricated / fraudulent research. You say that your supervisor has been very open about adding faked data to the paper - that seems very odd to be so open to a PhD student. Does your supervisor agree that you should write the thesis without the faked data?

I just think that the idea of adding the data to your thesis and hoping for the best is simply playing Russian roulette. Think carefully - don't use any of the faked data or the findings from it.

Take some rest - it's a bad situation you have found yourself in, but it's not the end of the world.

You need to get out with your PhD. My course of action would be to write up the thesis without the fake results (I omitted a paper I considered "irrelevant" that was more of a pet project by my supervisor - there was no forgery as such but it was a distraction from the main study that added nothing to it).

Once you find a job away from your old faculty and elsewhere, then it will be up to you whether to retract the papers. If it's serious then I would be tempted to retract, however, bear in mind that Universities close ranks and whilst the trouble maker would be moved on, they would also ensure you would not be employed by that university again as a whistle blower. There was a beauty of a case at a German University that demonstrated this point beautifully. I wish I could find the link.

You will have to explain why the papers were not listed or the data included in your thesis, however, you could argue thet your draft fo the thesis was already to advanced to rewrite to include and were outside the main focus of the thesis (i.e. extra studies).

I know of someone who omitted data from at least one paper that would have disproved the content. He listed a friend of mine as co-author.

In his case, my friend decided not to raise the issue for the simple reason life was too short. He simply wanted to more on from his job to pastures new and didn't want to be embroiled in any subsequent investigation.

I'm also aware of plagerism by Masters students who cut and past their data from the internet (they'd worked fulltime rather than study properly druing their project period) and have been told of two instances of PhDs based on fake data. It's not funny and not clever.

Ian

Your thesis can contain whatever you like.
You are under no obligation to include everything you worked on.
That is true even if you have published work not mentioned in your thesis.
I personally omitted two papers from my thesis.
I referenced both of them as "published works" and mentioned that I had excluded them for to keep the thesis length reasonable and also because they didn't fit the story I wanted to tell.
You can only be questioned on things you have actually written about.

Your much bigger problem has been highlighted above.
Your supervisor WILL be caught. It may be today, next week or in 20 years but he will be caught and anyone who published alongside him will be in trouble.
This needs dealt with right now IMO.
You need to take proper advice now. I don't think anyone on here can really help you.