I am sorry to hear of your circumstances. I am not a lawyer here but I just went through the divorce process without the assistance of any lawyers. Our circumstances were much simpler though: we did not have children or pets and we weren't after each other's money or assets.
First of all, were you and your soon to be ex-spouse (I'll just call him/her your ex for the sake of convenience) married in Hong Kong? What is this mutual divorce agreement signed in your lawyer's office though? Is it like a statement saying you and the ex have not lived together since such and such a date?
As emx said, to kick off the divorce proceedings in Hong Kong you need to file a petition. It could either be done on your own accord or it could be a joint application with your ex. You can do it through a lawyer too if you two cannot sort things out between yourselves, although many would highly recommend lawyering up because people are often at their nastiest when it comes to splitting assets and so forth (sweet couples can turn into nasty exes).
The CLIC flowchart is straightforward so do read through that closely. You may also want to familiarise yourself with the forms from the Judiciary too, which either you or your legal representative would ask you to sign. There are forms available for download - https://www.judiciary.hk/en/court_se...s/divorce.html - and there's a bit more detail on divorce proceedings too.
The decree nisi takes time as it has to go through the court system. If the case is not straightforward or there are points to contest then you and your ex may be summoned to court by the judge. The decree absolute is a matter of filling in a form, sending it back and the Family Court will eventually send you the paperwork indicating that your marriage has legally dissolved.
I hope this helps.