SPOILERS AHEAD!

To start the mod you need to have the prydwin in the commonwealth, either go about the game to kill Kellogg or force it to be there via the command "Player.setstage 000229E7 2000" to complete Kellogg's quest. After Kellogg is dead you can either go talk to the wastelander who is approaching you, or kill him and head to the prydwin to talk with paladin whitman to begin the BOS part of the quest.

What things mean:

00BIAQuestID <- This is the quest ID
"Quest Name" <- This is the quest name or description
Cells:
00BIACELLID <- This area holds the cell IDs for COCing to use them do "coc CELLID"
Stages:
10 - These are the stages
20 - The words next to them are the designer notes
30 - Thats why some of them are stupid
40 - Because I wrote them as reference while working on the mod
50 - Hope their clear enough for you sorry
60 - To use them do "player.setstage QUESTID STAGENUMBER"

LOS Side:

00BIALOSQ1
"Crawl Out Through The Fallout"
Cells:
00BIALOSBunker
Stages:
10 - Player has talked to the scout and is sent to the LOS Bunker
20 - Player has spoken with the gaurd and sent to find the tech
30 - Player has found the tech and is sent back
40 - Player has returned the gaurd and is let inside, and sent downstairs.
45 - Senior Staff Scene
50 - Player talked to ridley and completed the quest
99 - DEBUG FAIL STAGE

00BIALOSQ2
"Dark As A Dungeon"
Cells:
00BIALOSBunker
00BIALOSBunkerSublevel
Stages:
10 - Player said not yet for the quest.
20 - Player has started the quest and is sent to the bunker
30 - Player has entered the bunker, starting colvin follow.
32 - Player reaches door, starts colvin open door scene
34 - Optional find dogtags
36 - Starts colvin monolog 1
38 - Colvin comment on t51b and start of boss fight
40 - Colvin post combat comment
42 - Door locked, sends to find the key
44 - Entered VR lab, colvin comment.
46 - Key grabbed, sent to communications relay.
48 - Colvin comment on communications relay.
50 - read the terminal, moves colvin and sends back to colvin.
60 - talked to colvin sent to ridley
70 - Talked to ridley quest done.
75 - Colvin funeral done
99 - DEBUG FAIL STAGE

00BIALOSQ3
"A Good Man Is Hard To Find"
Cells:
00BIALOSBunker
00BIADavidFarmhouse
Stages:
10 - Talked to phillips, sent to clark
15 - recruited clark sends player to kill gunner squad
20 - gunner squad dead, sent to david
30 - Recruited david, sent to JC
35 - failed to recruit david, sent to JC
40 - Tallked to JC, sent back to phillips
50 - Returned to phillips, quest done
99 - DEBUG FAIL STAGE

00BIALOSQ3a
"Measure Of A Man"
Cells:
00BIADavidFarmhouse
Stages:
1 - Setup
10 - Talked to david sent to RR agent
20 - Found note return to david
25 - father son Scene starter
30 - Talked to david, Quest done

00BIALOSQ4
"Keep Knocking But You Can't Come In"
Cells:
00BIALOSBunker
Stages:
10 - Sent to kill whitman
20 - Killed whitman, return to phillips
30 - Talked to phillips, quest done.
99 - DEBUG FAIL STAGE

LOS Side Side Quests:

00BIALOSSQ1
"Shock And Awe"
Cells:
00BIALOSBunker
Stages:
10 - Started quest, sent to Lucas
20 - Player talked to lucas, sent to coil
30 - Found coil, sent back.
40 - Returned with parts, quest done.
99 - DEBUGFAILSTAGE

00BIALOSSQ2
"What The Doctor Ordered"
Cells:
00BIALOSBunker
Stages:
10 - Talked to the doc, sent to the patient
20 - Failed to heal the pateint
25 - Sucessfully healed the patient
30 - Returned to the doctor and completed the quest
99 - DEBUGFAILSTAGE

00BIALOSSQ3
"Porkin's Big Day In"
Cells:
00BIALOSBunker
Stages:
5 - Told to talk with porkins
10 - Quest started, told to get funnel cake.
20 - Got porkins his funnel cake

LOS Side VR Quests:

00BIALOSVRQ1
"Prepared For The Future"
Cells:
00BIALOSBunkerSublevel
00BIAVRTutCell
Stages:
10 - Quest Start
20 - VR Transfer
25 - 1st Target Spawned
30 - 1st target killed
35 - 2nd target spawned
40 - 2nd target killed
45 - 3rd target spawned
50 - 3rd target killed
55 - Three Targets Spawned
60 - Prime Target Killed
100 - VR Return

00BIALOSVRQ2
"There is only metro"
Stages:
Cells:
00BIALOSBunkerSublevel
00BIAVRSubway1
00BIAVRSubway2
5 - startup
10 - Move into sim
20 - VR Transfer
25 - Started mutant raid of looter base
30 - Sent to find the squad
40 - Found the squad, sent to find an exit.
50 - Found caved in exit, return to squad
60 - Sent further down the tunnel
70 - Guy wants a magnum
80 - Found magnum, starts next quest.
100 - VRReturn for VRQ4

00BIALOSVRQ3
"Red Dawn"
Cells:
00BIAVROrigin
00BIAVRSchool
Stages:
10 - Starts quest sends to the outside
20 - Went outside sends to the peoples
30 - Talked to the peoples sent on padding objective to find nuka
40 - Got padding object sends back to dude guy (UNUSED)
50 - Dude guy gives key, sends to talk to the other squad.
60 - Met squad quest complete.

00BIALOSVRQ4
"The very definition of failure"
Cells:
00BIAVROrigin
00BIAVRSchool
Stages:
10 - Tells player to get armor and in the vertibird
20 - Tells player to defeat commie prime
30 - Commie prime defeated simulation shutdown.

BOS Side:

00BIABOSQ1
"The Fate Of Steel"
Stages:
Cells:
00BIALOSBunker
1 - Sets Up NPCs
5 - Player kills LOS scout and points to whitman.
10 - Talked to whitman, sent to donahue.
20 - Completed Donahue's quest
30 - Started BOS assault
40 - Phillips dead, sends to whitman
50 - quest done
99 - Debug Fail Stage

00BIABOSQ2
"Not An Issue"
Stages:
10 - Moves magazines to their spawns 
20 - player picked up a magazine
30 - player returned to Donahue and turned in quest done