Asked editor for review prolongation to do further experiments, can't meet deadline. What do?
Based on the reviews and the willingness of the editor to provide an extension, your paper clearly is worth it for the journal. You should definitely contact the editor, briefly explain the problems (don't focus on excuses but on what remains to be done) you have had to meet the deadline and ask what can be done. It will be advantageous to provide a solid plan for the remaining work so that this is clear from the beginning to the editor. So assess the remaining work, make up a realistic plan for what is required and provide this to the editor. If all this requires the assistance of your advisor then plan it together. In the end, it will be up to the editor to provide an extension and a clear plan is necessary. 

In my own experience as editor, I much more appreciate realistic plans than optimistic ones that fail. In your case it seems as a case of force majeur and such things happen. I am, however, always suspicious of long excusing accompanying letters since I really do not care about the reasons but need to focus on the timing of revisions for planning issues and the like.