Fallout 4 Quests

General information
There are a total of 140 quests, of which:
 * 13 are from the Main quests
 * 34 are Non Faction Side quests
 * 22 are from the Brotherhood of Steel
 * 26 are from The Minutemen
 * 21 are from The Railroad
 * 24 are from The Institute
 * 4 are from Companions

Act 2
After completing The Molecular Level, the main quest's structure becomes similar to the one from Fallout: New Vegas. There are four different branches, one for each faction, and certain events in those quests can make certain factions hostile to the Sole survivor, thus locking them from those branches and failing all of that faction's on-going quests. In some situations, this can be delayed (or even accelerated) with certain actions or certain dialogue choices. Should the player decide to oppose The Institute by supporting any of the other three factions, the main quest ends with The Nuclear Option quest (there are actually three variants of the same quest, one for each faction opposing The Institute). However, should the player join and support The Institute, the main quest ends with the Nuclear Family quest.

The following quests become available after completing The Molecular Level:
 * Institutionalized (The Institute branch) - starts automatically
 * From Within (Brotherhood of Steel branch) - given by Elder Maxson if the player completed Show No Mercy
 * Inside Job (The Minutemen branch) - given by Sturges if the player completed Old Guns
 * Underground Undercover (The Railroad branch) - given by Desdemona if the player joined the Railroad by completing the Tradecraft quest

Side quests
These are non-affiliated side quests.

Miscellaneous quests
These quests are displayed under the section "Miscellaneous" of the Pip-Boy.

Settlement quests
There are a number of misc quests associated with settlements. Most of them are settlement defense quests that start automatically and will fail if you don't complete them within a certain time.