How can I stop students being able to go to the last page of the flow which is their certificate if they have not achieved the pass mark.

Hi Monica,
That depends mostly on what navigation resources the students have in the first place. Do they have an unrestricted menu? Back and Next buttons on a Master?

Also, what constitutes a pass mark in this lesson? Is there a quiz they must pass? Or simply visit all the other pages in the lesson? Or are some pages more involved than others?

There are a few different approaches you can take:

1. Put the certificate on its own page, and restrict access to that page.
2. Put the certificate on its own page, and allow them to get to that page at any time, but do not show the certificate until they have passed the lesson (maybe show a message saying they haven't passed yet). This is probably what I would recommend because it's the easiest to implement.
3. If you're using a quiz, maybe build the certificate into the passing feedback.

Hope that helps. If you can tell us more about what is needed to pass, and what navigation features your lesson currently has, we can offer more specific advice.