SPOILERS AHEAD!

Chapter 2 starts immediately after chapter 1 ends, either talk to Colvin or Phillips to start it after defending against the brotherhood attack.

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"

00BIAC2MQ1
"Straighten Up And Fly Right"
Cells:
00BIALOSBunker
00BIALOSBunkerHanger
Stages
5 - Sent to talk to Colvin
10 - Sent to find Ridley
20 - Found ridley, sent back
25 - Moves ridley n colv, shhh
30 - Starts intro Convo
35 - Sends the gang to the hanger, also unlocks the hanger
40 - Starts hartstock intro
42 - Internal For Dialog
45 - Tells the player to get the vertiparts
50 - Got the vertiparts, sending back.
55 - Now he needs coolant
60 - Got the coolant sent back
65 - Starts Ridley Hartstock Argue Scene
70 - Now he needs a power manifold
75 - Got the power manifold
80 - They're ready to go when the player is
90 - Moves everyone to the vertibird
95 - Starts verti convo
100 - Verti Crash but convin likes
200 - Verti Crash but convin dislikes

00BIAC2MQ2
"Far From Anywhere"
Cells:
00BIAChap2ColvinBunker
00BIACanadianCottage
Stages:
5 - starts scenea
10 - Sends to little canada
15 - Wolf Scene
20 - Tells to look around (implies doing the quest)
30 - Found Triage Kit, sends back to Colvin
40 - Returned to colvin, quest over.

00BIAC2MQ3
"Old Friends"
Cells:
00BIAChap2ColvinBunker
00BIAChap2OutcastMotorpool
Stages:
10 - Colv Sends to Find Rifle
15 - Found Rifle
20 - Wake up crash scene, sends to grab medkit
25 - Found Medkit
30 - Outcasts jump the player.
40 - Tells to follow the outcasts
45 - Dead Bear Scene
50 - bear scene done, lets keep going
55 - Tells to disarm
60 - Disarmed, allowed in
65 - Starts outcast intro
69 - Internal for dialog
70 - Sent to Peirce
80 - Sent back to Rockfowl for final convo
90 - Starts final dialog
92 - Internal for dialog
100 - Player is now forced to do outcast bidding, quest over.

00BIAC2SQ1
"Great White North"
Cells:
00BIACanadianCottage
Stages:
10 - Tells to speak with the robot
12 - Internal stage for saying no
20 - Sends to invesigate the town
30 - found shopkeeper, across from the church sending to hardware
40 - found hardware, sending to poutine
50 - Found poutine, sending to bar
60 - Got beer, sending to poutine
70 - Got poutine, sending to hardware
80 - Got hardware, sending to shopkeeper
90 - Got info, sending to look at cottage and graveyard
100 - Unlocked cottage, sending inside
120 - read terminal, sends to fight
130 - Fight won, sent back to gutsy
140 - Gutsy happy, quest done.
999 - Fail Stage


00BIAC2MQ4
"Old Wounds"
Cells:
00BIAChap2OutcastMotorpool
00BIAChap2CanSimChurch
00BIAChap2SynthCaveHideout 
00BIAChap2ColvinBunker
Stages:
10 - Sent to find the synths
15 - Found church sent to find body
20 - found body sent inside church
30 - Found note sent to cave
40 - Found cave, starting sermon
45 - sermon over, tells fred to sit
46 - Internal for dialog
50 - Done talking to fred, sends back out.
60 - Found colvin, follow him home
70 - Back home, talking to colvin now.
75 - Internal for dialog
100 - Quest over.

00BIAC2MQ5
"Come Together"
Cells:
00BIAChap2OutcastMotorpool
00BIAChap2SynthCaveHideout 
00BIAChap2ColvinBunker
Stages:
10 - Sends back to the outcasts.
15 - Starts outcast scene.
20 - Sent to Colvin.
25 - Conflict path, sending to Q5B
30 - Work together path, sending on to talk to the synthos
35 - starting bible story
40 - Synths need some stuff, ask the player to get them, sending to Q5A
50 - Q5A Done, sending back to outcast base
55 - Moves everyone to their place
60 - Starts outcast planning scene.
65 - Internal for saying not ready
70 - Outcast planning scene done, quest done.

00BIAC2MQ5a
"Poems, Prayers And Promises"
Cells:
00BIAChap2SynthCaveHideout 
00BIAChap2CanSimChurch
Stages:
5 - Internal for dialog
10 - Sends to find the medical supplies
20 - Found medical supplies, sends to the church, also protectron ambush
30 - Got personal effects, sends back to fred, also ghoul ambush in church.
40 - Talked to Fred, quest done, Q5 can continue.

00BIAC2MQ5b
"Dont Fence Me In"
Cells:
00BIAChap2ColvinBunker
00BIAChap2OutcastMotorpool
00BIAChap2SynthCaveHideout 
00BIALOSBunker
Stages:
10 - Tells to talk to Colvin
20 - Talked to colvin, time to take out the outcasts.
30 - Outcasts are dead, great work! 
35 - Time to take out the synths
38 - Starts fredconfront scene
40 - Tells to kill synths.
45 - Let synths run away.
48 - Tells to talk to Colvin
50 - Synths are gone, now to find a way to blow open that cave in.
55 - Player found the explosives
60 - Player is teld to set up the bomb
65 - Player set up the explosives
70 - The way is clear, time to go home.
75 - Sends everyone home.
80 - Player is back in the commonwealth, sends back to site gamma
90 - Starts final scene.
100 - Final scene done, quest done.
999 - Decided to not kill everyone.

00BIAC2MQ6
"We'll meet again"
Cells:
00BIAChap2OutcastMotorpool
00BIAChap2OutcastMotorpool
Stages:
10 - Starts up all the AI packages, time to head out
15 - Defeated sentry, tells to talky
20 - Sent inside.
30 - Tells to find a way to disable lockdown
40 - Lockdown disabled, sets up fred death and robot ambush.
50 - Fred death over, sent up.
55 - Robot ambush one
65 - Robot ambush two
69 - Server room setup
70 - Found server room
75 - Sends morgan up
80 - Sets up the choice
105 - ColvShoot
108 - ColvShootDone
110 - Choses to leave sarah dead
120 - choses to revive sarah
125 - Sarah back, sends up
140 - Sets up boss fight
145 - Starts boss scene
150 - Starts Morgan Boss Fight
160 - Morgan defeated, sent back down.
165 - Moves da boys back down
170 - New plan formulated, quest over, next quest started.

00BIAC2MQ7
"Flying Low"
Cells:
00BIAChap2AirfeildHanger
00BIALOSBunker
Stages:
10 - starts up and tells to go to airfield
20 - At airfeild, take on the robots
30 - Robots dead, talk to ridley
40 - Ridley talked to, sent to find gaskets
50 - gaskets found, sent back to ridley
60 - Talked to ridley, tallk to ivy
65 - Talked to ridley, talk to sarah
70 - Time to go home
80 - Sent home, starts landing scene
90 - Sent back to site gamma
92 - Moves everyone to their spot
95 - back at site gamma, final scene.
100 - Quest done
200 - Quest done + Sarah

00BIAC2Sarah
"The Way It Used To Be"
Cells:
00BIALOSBunker
00BIALOSBunkerHanger
Stages:
5 - sends to sarah
10 - Tells to talk to Colvin.
15 - Internal for dialog
20 - Tells to follow colvin
30 - Starts the sad scene :(
40 - they talkied, is over now