The third pass: Virtually re-implement the paper
This pass requires great attention to detail. You should identify and challenge every assumption in every statement.
If you are a beginner then this pass probably takes 4 to 5 hours.
Read the paper in its entirety and question every detail. Make the same assumptions as the authors and re-create the work from scratch. Re-implement the steps in your head or use any tool.
At the end of this pass you should be an expert and know the paper’s strong and weak points.