May they delay for a long time the decision of a submitted manuscript of someone that already sent a paper which didn't pass plagiarism check? As I already shared in this question, I have submitted a paper in January
of the last year to a high-rank journal and they decided on my paper with reject and resubmit. I worked very very hard and prepared a revised version of the manuscript which significantly improved the paper with a near 50 pages response letter to reviewers. 

Unfortunately, in this university which I am getting my Ph.D., they have an obligation that advisor, must be the corresponding author. Two students of my advisor, which I don't know personally, submitted a paper to the same journal a short time after the decision of my manuscript. After less than a week, journal sent a letter to my advisor which is also the corresponding author of their manuscript that their paper didn't pass the plagiarism check. By my investigation, I found out that they copy-pasted some parts of their introductory paragraphs from other papers. My advisor sent a letter to EIC telling him that this problem was due to not having plagiarism checker software. He is the second author in my paper and third author in the other paper and corresponding author for both of the papers. 

I have now waited a long time for the decision of my manuscript. One of the professors in this university, yesterday told me that they may not have sent the paper to the reviewers and make you wait for a long long time. Then if you mail them, they will reject your paper. It is a punishment for your advisor. Otherwise, they will make you wait for 12 to 15 month just for punishment and then without review reject it. 

It was a nightmare for me as I am under immense pressure for my job and my graduation. I agree that my advisor is an irresponsible and ignorant person. But I didn't do anything wrong. Just honest very very hard work. 

May they delay for a long time the decision of a submitted manuscript of someone that already sent a paper which didn't pass plagiarism check?
Is there any such policies or behavior in journals?
What should I do?
The people who run good journals are (i) professionals, (ii) people. From the first follows that it's not professional or appropriate to sit on a paper for a year without sending it out to reviewers or making a decision as punishment. That's just not ethical. From the second it follows that the editor is probably not going to bend over backward to ensure the paper gets dealt with today instead of tomorrow. In any case, your characterization of editors as these kinds of vindictive monsters out to get you is incorrect -- that's not the kind of person who would be appointed as an editor.

Either way, there is nothing wrong with writing an email to the editor and asking what the status of a paper is. That happens every day, and it's part of the job of an editor to deal with this in a professional manner. So go ahead.