OS X 10.11.4 TheBrain v220.127.116.11
1. If v9 is running but the brain where the thought connected to the Local Thought URLs is closed, then the URL, when clicked in another app (e.g., Reminders) will open the target Brain in v9 with the thought in focus, but the action resets the layout of the panels in TheBrain. E.g., I always have the window configured with Notes on the right and the Plex on the left. Clicking the URL activates the target thought with Notes on the bottom and the Plex on top.
2. If v9 is running, and the thought URL is clicked, TheBrain opens the target brain/thought silently: the app is not brought to the foreground. I would expect that clicking URLs will bring TheBrain into the foreground as the active window.
3. If v9 is not running, clicking the URL will cause v9 to bounce in the Dock, appear to open (though it cannot be brought to the foreground) and then terminate. The Console has this message in that case:
5/22/16 3:43:46.901 PM TheBrain 9: warning: exception inside UnhandledException handler: Object reference not set to an instance of an object