In this case, you may wish to familiarize yourself with examples of other reviews done for the journal, which the editor should be able to provide or, as you gain experience, rely on your own evolving style. Sometimes they will ask you to address specific questions in your review via a questionnaire.
Or they might want you to rate the manuscript on various attributes using a scorecard.
Often you can't see these until you log in to submit your review.
So when you agree to the work, it's worth checking for any journal-specific guidelines and requirements.
Such issues include: After the initial read and using your notes, including those of any major flaws you found, draft the first two paragraphs of your review - the first summarizing the research question addressed and the second the contribution of the work.
If the journal has a prescribed reporting format, this draft will still help you compose your thoughts.For example, it's impossible to argue that there is a conflict in current understanding by referencing articles that are 10 years old.Authors may make the case that a topic hasn't been investigated in several years and that new research is required.Of course, you may still decide to reject it following a second reading.The benchmark for acceptance is whether the manuscript makes a useful contribution to the knowledge base or understanding of the subject matter.It is also important at this stage to declare any potential Conflict of Interest.The structure of the review report varies between journals.Even if you are coming to the opinion that an article has serious flaws, make sure you read the whole paper.This is very important because you may find some really positive aspects that can be communicated to the author. A full read-through will also make sure that any initial concerns are indeed correct and fair.It need not be fully complete research - it may be an interim paper.After all research is an incomplete, on-going project by its nature.