As far as I understand, when they initiate the security check, they conduct one final eligibility assessment and add a note to the file. This might be the "Stage 2 eligibility assessment." The most recent note states: "protected persons processing – non-complex processing assessment."
And below that:
Eligibility: passed
Security: in progress
Biometrics: passed
Criminality: passed
Medicals: passed – exempt
As I understand it, at this stage they are completing a final eligibility assessment and are now waiting for the security clearance to be completed. Once the security clearance is granted, a final decision is issued.