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You can quarantine at your final destination.
If you are cleared to fly, you may board a connecting flight to reach your final destination. You do not need to quarantine (self-isolate) before connecting, unless your final destination requires you to quarantine at a designated location first.
https://travel.gc.ca/travel-covid/travel-restrictions/provinces#connecting
However, like any traveller, if you start showing symptoms during your layover, you will not be allowed to board the connecting flight without public health approval.