There are 4 factions in Fallout 4: Minutemen, Brotherhood of Steel, Railroad, and Institute. In order to 100% the game you have to side will all 4 factions and complete their questline. The only issue is you cannot do this in one straight playthrough as you will become enemies with certain factions as you continue other factions questlines.

Because of this I have outlined "Safety Saves" which are save files you create before making major decisions so you can reload and side with the other factions. Using this guide you will be able to achieve all the story based achievements on one character without having to start the game over.

One last thing is there are two end game achievements that should be mentioned:

• The Nuclear Option
  
• Prepared for the Future

These two achievements are gained after completing a quest called The Nuclear Option that comes at the end of the Minutemen, Brotherhood, or Railroad questline. Obviously doing this quest for each faction would make no sense since you are doing it 3 times and only have to do it once for the achievement. Because of this I recomend choosing whichever faction you like the best and completing this quest for them. (Completing the institute questline only gives you Prepared for the Future and not The Nuclear Option).

Notes:

Bolded achievements should be completed before doing The Molecular Level quest. You can do them all without screwing up allegiances with any factions and being on good terms with all.

• War Never Changes
  
• When Freedom Calls
  
• Unlikely Valentine
  
• Reuinions
  
• Dangerous Minds
  
• Hunter/Hunted
  
• The Molecular Level
  
• Institutionalized
  
• The Nuclear Option
  
• Prepared for the Future

• The First Step
  
• Sanctuary
  
• Taking Independence
  
• Old Guns

• Semper Invicta
  
• Blind Betrayal
  
• Ad Victoriam

• Tradecraft
  
• Underground Undercover
  
• Rockets' Red Glare

• Mankind-Redefined
  
• Powering Up
  
• Nuclear Family

The story quest "The Molecular Level" requires you to make a ultimatum on which faction you want to side with. When you recieve the objective to talk to Virgil in this quest, make a save file which will be Safety Save #1. This will be your safety save that you will fall back on to choose a different faction. You will want to have all the achievements printed in bold as you make this save. Refer to the list above.

Now that you are at the point to choose a faction, you have 2 options. Choose the brotherhood of steel, or choose the railroad. You CAN choose the minutemen however you should already have all the minutemen achievements at this point so for the sake of going for 100% completition the minutemen will not be an option here.

This guide goes in order of siding with the brotherhood first, then the railroad. You can do it the other way around it does not matter. However you will want to side with the institute along with the railroad since their paths interweave.

Talk to the Brotherhood during The Molecular Level and build the teleporter with them. Continue working with the Brotherhood until you get these achievements:

• Blind Betrayal
  
• Ad Victoriam

Continue with the Brotherhood to get The Nuclear Option and Prepared for the Future then reload Safety Save #1 and choose the Railroad.

Talk to the Railroad during The Molecular Level and build the teleporter with them. You will get a quest called Underground Undercover which you will want to do until you reach the objective "Continue working with Father". At this point keep doing institute quests until that objective is marked as complete. During this period you will get these achievements:

• Mankind-Redefined
  
• Powering Up

After this you will get a quest "End of the Line" and you can continue with Underground Undercover. If you do End of the Line, you will side with the Institute. If you finish Underground Undercover, you side with the Railroad. You will want to make a save file which will be Safety Save #2 so you can get both paths done. Continue working with the Railroad until you get these achievements:

• Underground Undercover
  
• Rockets' Red Glare"

Continue with the Railroad to get The Nuclear Option and Prepared for the Future if you have not already then reload Safety Save #2 to finish the Institute.

Now you will start the End of the Line quest. Continue working with the Institute until you get these achievements:

• Nuclear Family

Continue with the Institute to get Prepared for The Future if you have not already.

With this you are finished with all factions and should have every quest achievement, congrats!