Banished from the Institute

Banished from the Institute is a side quest in Fallout 4 that is given for becoming enemies with the Institute.

Detailed walkthrough
There are multiple ways to get banished (all of which first require fully completing Institutionalized).
 * Kill Father or any other named Institute personnel.
 * Talk to Father negatively at the end of The Battle of Bunker Hill.
 * Board the Vertibird that spawns on the Prydwen to Mass Fusion with the Brotherhood of Steel during Spoils of War.
 * Support the Minutemen during Pinned. (This option is only available if Taking Independence has been completed)

To exit the Institute, simply head for the central elevator and head up to the relay room. Look for the bright red Emergency Relay button on the side of the main console just outside the relay room and push it to activate the emergency relay. Walk into the relay room and the countdown begins, upon reaching half-way through the countdown, Father will speak over the intercom. If he was killed, an Institute scientist will speak instead, expressing horror at the fact that the Sole Survivor has killed their own son, and tells them to run and promises to kill the player character once found.

If outside of the Institute, return to that location. The Sole Survivor will teleport back to the relay, and Father will speak over the intercom.