Last month Microsoft released the iOS 9 Intune extension for ConfigMgr. At a customer with Hybrid scenario (ConfigMgr with Intune) however the iOS 9 extensions was missing. Whenever starting the ConfigMgr console, no new message are displayed.
We logged a call with Intune Support and the following did the trick:
Start SQL Management Studio and run the following queries against the SMS database.
Select * from CFDMetadata where FeatureID = 'FFFF4E99-5BD9-4A82-BC9F-7864FCAEA519'
update CFDMetadata set MinCMVersion = '5.00.8239.1000', MaxCMVersion = '5.00.8239.9999', MoreInfoLink = 'https://go.microsoft.com/fwlink/?LinkId=330435', ReleasedDate = '2015-09-11 09:09:00.000' where FeatureID = 'FFFF4E99-5BD9-4A82-BC9F-7864FCAEA519' and FeatureVersion = 300001214
After starting both queries, the iOS Intune extension became available. Hope it helps!