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:
 * Refuse to work with the Institute when the Sole Survivor meets Father for the first time. This will not trigger the Banished from the Institute quest, it is an optional ending of Institutionalized.
 * Kill any 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 the Sole Survivor is the general of the Minutemen, otherwise there will be Gunners that will attack on sight.)
 * If the start of the quest is triggered through console commands while outside the Institute, you will not be able to relay in. Instead, you will need to travel to the C.I.T. ruins and the quest will complete itself.

To exit the Institute, simply head for the elevator and head up. Look for a bright red button in the room and push it to activate the emergency relay. Walk into the relay 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.