We have submitted a manuscript in a Finance journal. Within 1.5 months, they gave us the comments of two reviewers. The Reviewers gave positive remarks but wanted some correction. We carefully scrutinized both reviewers suggestions and found that they have contradictory demand. Hence we follow the second reviewer's comments and made changes according to his suggestion. We also explained why we could not follow the first reviewer's suggestion. After resubmitting, within one-week editor again send us feedback ( or review) that since we did not follow the first reviewer's suggestion the first reviewer gave a suggestion to reject our paper. So the editor wants us to change our paper again. Again, we thoroughly explained why we fail to comply with the first reviewer's suggestion and resubmitted the manuscript (third time). After that, it has been 3 months there are no changes in status. Status shows "with review" Do you think taking three months after the third submission is natural? Should I mail the editor to speed up the process?
I do not see anything unusual or particularly alarming in this situation. Your first review arrived very quickly — compared to Mathematics, where a first review can take 15-18 months in some journals.
It is not unusual for reviewers to make remarks which appear contradictory. Sometimes it is possible to find a compromise to pacify both; sometimes (as in your case) it is necessary to rebut the criticism. Rebuttals are never easy and the suggestion of the first reviewer to reject a paper is not completely unexpected. Now the decision falls on the Editor, who has to either side with you (and potentially lose their Journal the Reviewer One) or side with Reviewer One and reject your paper. It is not an easy decision, and it requires for Editor to personally read the paper, or to invite another reviewer to join the fun. Whatever they are doing, three months does not seem overly long yet to me.
tl;dr: It's best to wait patiently.