A finished manuscript is submitted to a particular journal that the author or authors want to get published in. The editor of the journal reviews the article and then either passes it on to a group of usually two to four peer reviewers or rejects it. If it is passed on to peer reviewers, they will read it and give feedback as to the strengths and weaknesses of the methodology of the experiment, the content of the article, etc. After it is peer reviewed, the article goes back to the publisher again. At this point, it is either accepted with no revision, rejected, or given back to the author(s) for recommended revisions.
The first step in the process is the authors making a rough draft of the manuscript which includes all the information and details they wish to submit to a journal. Then they choose a journal based on several factors. These include the subject matter of the research, the prestige of the journal, the audience the journal reaches and impact the article might have, and past connections with a particular journal.
Journals with high impact results are considered more desirable. A journal that is considered high impact has more of their articles referenced compared to the total number of citable articles compared to other journals. This means more exposure for the authors, more notability and perhaps a better chance of being funded.
Articles are accepted based on the direction the journal wants to go in and the basic philosophy of the journal. If the article is rejected at this point, the author has to find another journal to submit to.
The peer reviewers are considered established professionals who are also published in the field related to the journal. They are chosen by the editor of the journal and are anonymous to the authors, while they are aware of who the authors of the manuscript are.
The peer reviewers watch for several things when reading the manuscript. This includes whether the research is relevant, whether data supports the hypothesis, whether the methodology is sound, whether figures and graphs match the statements in the paper, etc.
They write up their analysis of the article and give it back to the editor. At this point, the editor will accept it, reject it or return it to the author for revisions. If it is returned to the author, they can make revisions and resubmit as needed until it is ultimately either rejected or accepted for publication.