I have a Fortigate FW and I would like to connect it to zero tier without having to install it on endpoints, has anyone tried or know something like this and could they help me?
Check out my article at Zerotier & Mikrotik design concept - Infrageeks
In your case, ignore the Mikrotik part and go to the part for routing from an existing router (pfSense in my case) and the topology should also work using replacing pfSense with your Fortigate.
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