What to do with papers after misconduct allegation was resolved? I was alleged in scientific misconduct in form of authorship abuse. More details are in my previous questions

How to respond to allegations of misconduct in authorship dispute?

Should I put my supervisor as coauthor of a paper?

The good news is that the investigations have ended in the inquiry stage (the dean have informed me by email). 

There are several probable reasons why they have stopped:


The article was indeed done with different methodology, which had nothing to do with the approach described in the grant application.
At the interview I have revealed several facts of abuse, namely I was ordered to work on the projects not connected to my funding project.
They are afraid I could become a whistleblower.


After receiving the confirmation from the dean, I immediately informed the editor of the journal. Unfortunately, the editor rejected the manuscript, stating that:


  This is useful information for us, but the question before the journal is not one of personal scientific misconduct, but rather whether the authorship on the paper is the correct one, and whether we should proceed with the external review process, which may lead to its eventual acceptance and publication. 
  
  Based on the information available, we have decided not to go further with the review of your manuscript.  There are still significant concerns being raised about whether the manuscript should have been submitted with its current authorship, and we do not believe there is any clear path to removing these concerns.  The scientific reviews we have received are mixed and would place the manuscript in an unclear position regarding acceptance or rejection based on its content.  These two factors together give us sufficient cause to issue a rejection.  Because the manuscript did not reach the publication stage, no other action is necessary, and we would like to also consider the case closed.


My questions are: 


Should I try to resubmit the manuscript as is into some other journal; should I redo all the calculations, reanalyze, and rewrite it first; or should I just abandon it?
I have another manuscript, for which my ex-supervisor sent me an email stating that "he assumed that I was going to publish it by my myself", in spite of the fact that he supported me. This seems to be the evidence that he resigns his authorship. Should I try to publish it also?
Can they reopen the misconduct case if they would like to do that?
If you would like an academic future, you should ask these questions your (former?) PI, and do your best to make up. 

Some answers to related earlier questions you asked gave you advice that saw this only from a David taking on Goliath perspective, and wrote what I felt would only further egg you on. With additional information added in the newer questions, however, you really found yourself in the extremely rare case of your PI taking action against you at your own school. It is time to stop acting on guesses and interpretations, with some Internet forum feedback. You need to get a clear answer from that PI, ideally in writing: for 1 and 2, ask if this means he agrees you can go ahead and submit the 2 papers under your single-authored name? 

However, that isn't what I would do. 2, at least, could be read as a conciliatory outreach by your PI: I assume you want to publish this by yourself? (...but do tell me that no, you would like to go together). 

Even if that is not true, publishing something (anything) with your PI now matters more than a publication by yourself. You write they are "afraid" of you. They are not. Whistleblowers (if you even could blow a whistle) are a nuisance and embarrassment, rarely more; and in the cases in industry I know of (a friend was a fairly high profile one in banking), they eventually only come back to bite the whistler. It may take years and seem differently; but they eventually do. 

Justly or not, the whole incident reflects poorly on all participants (a petty adviser; and a student setting off a petty adviser). For an academic future, in all cases I am familiar with you need your adviser's support. You had a falling out; you should try to mend it. The situation will not help the PI to recruit in the near future; and how are you going to get recommendations that matter? You both have an interest in making up: that is what you should focus on. It may be hard, it may be impossible; but it doesn't seem that you have tried, or tried hard enough. It's your life and future, and phyrric victories and a single publication don't matter in the big scheme. 

If you really just want to know if you can ignore all this, and publish alone  based on that email and the result of the proceedings: I find it risky, but not very so as there is no way your PI is going through with another case...at least it's extremely unlikely. But I don't think that's what will serve you best.