Do these steps IN ORDER.

Underlined lines are important steps you should follow in order to not miss certain AI comments. A lot of these are "shared" messages, such as "Close examination", but I included them all in the list in case you missed one instance of it. I still recommend checking them all in case they are somehow unique.

I did not include every place you can run out of energy, only the fastest place with the most AI messages (which is running out of energy to poison). This is mainly to save yourself 4 hours of doing nothing but sitting still.

List of AI lines not in the game: http://pastebin.com/q9yWdGtq

Multiple AI messages are at the very start (once the lights turn on after the phone call (you can skip the phone call). Do not skip ANY AI messages until the AI stops talking.
Automatic message after standing up
Do not pick up the transport card yet.
AI Chip: Mission Briefing
AI Chip: Environ Scan (inside apartment, before changing hairstyle)
AI Chip: Environ Scan (after changing your hairstyle)
AI Chip: Environ Scan (anywhere but inside the apartment)
Waiting for 5 minutes: Late first warning (anywhere in Caldoria)
Waiting for 10 minutes: Late 2nd warning (anywhere in Caldoria)
Getting into the Transporter WITHOUT the transport card
AI Chip: Hint #1 (In the Transporter WITHOUT the transport card)
Now pick up the transport card.

AI Chip: Mission Briefing (outside Command Center, pre-rip)
AI Chip: Environ Scan
AI Chip: Mission Briefing (sitting down in Command Center, pre-rip)
AI Chip: Mission Briefing (post-rip, outside of Pegasus)
AI Chip: Mission Briefing (inside Pegasus)
AI Chip: Environ Scan (inside Pegasus)

AI Chip: Mission Briefing
AI Chip: Environ Scan
Wait around for 10 minutes until you hear the 'tectonic plate' AI speech.
Do not flip the switch yet.
Move towards any cliff (Should be automatic after forced pterodactyl movie)
Move towards cave with dinosaur (when the flashlight clicks on, the AI message will play)
Step inside the cave (automatic message)
AI Chip: Environ Scan (inside dinosaur cave)
AI Chip: Hint #1 (Click hand scanner without flipping switch)
Now flip the switch.
AI Chip: Hint #1 (after crossing the bridge, 'Examination of inventory/biochips')
Automatic message when getting the disc

AI Chip: Mission Briefing
AI Chip: Environ Scan (outside Pegasus)
AI Chip: Hint #1 (right before you reroute robots)
AI Chip: Hint #2 (right before you reroute robots)
AI Chip: Hint #3 (right before you reroute robots)
AI Chip: Mission Briefing: (after you reroute robots)

Automatic message when getting poisoned
SAVE FIRST: Stay poisoned, Low energy warning (50%) (10 minutes)
Stay poisoned, Message about 'poison shutting down nervous system' (between 50% and 25%)
Stay poisoned, Low energy warning (25%) (15 minutes)
Stay poisoned, Low energy warning (5%) (19 minutes) (Load save)
AI Chip: Mission Briefing
AI Chip: Environ Scan (in first room)
AI Chip: Hint #1 (while poisoned)
AI Chip: Hint #2 (while poisoned)
AI Chip: Hint #3 (while poisoned)
Automatic message when taking dart out
AI Chip: Hint #1 (while solving the molecule puzzle)
AI Chip: Hint #1 (any screen near the Nitrogen/Argon canisters, 'Close examination')
Do not pick up the Sinclair keycard yet.
Get the Nitrogen Canister.
AI Chip: Environ Scan (in hallway)
Automatic message when facing area with personnel one square ahead ('biorhythms')
AI Chip: Hint #1 (when facing area with personnel one square ahead, 'audio amplification')
AI Chip: Hint #2 (when facing area with personnel one square ahead, 'must not compromise your mission')
AI Chip: Hint #1 (when facing Sinclair's office door WITHOUT keycard, 'Useful item elsewhere')
Now pick up the Sinclair keycard.
AI Chip: Hint #1 (when facing Sinclair's office door WITH keycard, 'Examination of inventory/biochips')
AI Chip: Environ Scan (inside Sinclair's office)
AI Chip: Hint #1 (facing wall with assault rifle, 'Close examination')
Automatic message after picking up assault rifle
AI Chip: Hint #1 (facing brochures on desk, 'Close examination')
Automatic message when facing blasted door
AI Chip: Hint #1 (when facing blasted door WITHOUT crowbar, 'Item not in inventory')
AI Chip: Hint #2 (when facing blasted door WITHOUT crowbar, 'item found in another time zone')
AI Chip: Hint #3 (when facing blasted door WITHOUT crowbar, 'use the crowbar found in Mars')
Leave and go to NORAD.

Automatic message when entering
AI Chip: Mission Briefing
AI Chip: Environ Scan (first room)
AI Chip: Hint #1 (while breathing sleeping gas WITHOUT oxygen mask, 'filter out air')
AI Chip: Hint #2 (while breathing sleeping gas WITHOUT oxygen mask, 'oxygen mask in Mars')
AI Chip: Hint #3 (while breathing sleeping gas WITHOUT oxygen mask, 'functions of oxygen mask in Mars')
Automatic when taking gas canister out
AI Chip: Hint #1 (when holding the gas canister)
AI Chip: Hint #2 (when holding the gas canister, 'must not compromise your mission')
Fill Nitrogen and go to Mars.

AI Chip: Mission Briefing
AI Chip: Environ Scan (shuttle dock)
Do not pick up the ID Card yet.
Automatic message when facing the Ore Processing room exit ('low oxygen beyond this point')
AI Chip: Environ Scan (in maintenence tunnels, 'Morimoto Mars Colony')
AI Chip: Hint #1 (facing the area where the crowbar is, 'Close examination')
Grab the crowbar.
AI Chip: Hint #1 (facing the front of the transport pod WITHOUT ID Card, 'Useful item elsewhere')
AI Chip: Hint #2 (facing the front of the transport pod WITHOUT ID Card, 'ID Card in main entrance')
AI Chip: Environ Scan (Reception area, Main Entrance)
Automatic when facing Colony Entrance door
AI Chip: Hint #1 (when facing Colony Entrance door, 'don't risk mission by talking to others')
AI Chip: Hint #1 (when facing ID Card, 'Close examination')
Now pick up the ID card.
Automatic message when facing Maintenance Transport door after taking the transport car ('strong temporal flux')
AI Chip: Hint #1 (when facing oxygen mask, 'Close examination')
Automatic message when picking up oxygen mask.
AI Chip: Hint #1 (with oxygen mask in inventory, 'oxygen supply in NORAD')
With the oxygen mask, leave and go to WSC.

AI Chip: Hint #1 (when facing blasted door WITH crowbar, 'Examination of inventory/biochips')
AI Chip: Hint #2 (when facing blasted door WITH crowbar, 'use the crowbar found in Mars')
AI Chip: Hint #1 (after opening door, without moving, WITHOUT Shield biochip, 'Biochip found in NORAD')
Leave and go to NORAD.

Fill oxygen mask and enable it.
AI Chip: Environ Scan (in the hallway)
Don't do launch prep yet.
AI Chip: Hint #1 (click the panel next to the sub BEFORE doing the Launch Prep)
AI Chip: Environ Scan (Launch Prep room)
AI Chip: Hint #1 (face launch Prep screens without zooming in, 'Close examination')
Now do launch prep.
Automated message when facing the Retinal Scanner door.
AI Chip: Hint #1 (when facing retinal door WITHOUT Retinal Biochip, 'item found in another time zone')
AI Chip: Hint #2 (when facing retinal door WITHOUT Retinal Biochip, 'Retinal Biochip in WSC')
Leave and go to Mars.

Head to the spot where the 2nd robot appearance is.
After seeing robot before the reactor, automatic message when stepping onto the transport pod tracks with no car (this is also a death)
Automatic message when opening Shield Generator door
AI Chip: Hint #1 (when in reactor WITHOUT Shield Biochip, 'item found in another time zone')
AI Chip: Hint #2 (when in reactor WITHOUT Shield Biochip, 'Biochip found in NORAD')
Leave and complete WSC.

Head to the door you open with the crowbar.
AI Chip: Environ Scan (after getting shot, on moving walkway)
AI Chip: Environ Scan (after entering next area after moving walkway, 'Center auditorium complex')
Automatic message when facing the purple door you open ('strong temporal flux')
AI Chip: Hint #1 (on the catwalk)
AI Chip: Hint #2 (on the catwalk)
AI Chip: Hint #3 (on the catwalk)
Automatic message when robot dies.
Leave and complete NORAD.

Head to the retinal scanner door.
AI Chip: Hint #1 (when facing retinal door WITH Retinal Biochip, 'Examination of inventory/biochips')
AI Chip: Hint #2 (when facing retinal door WITH Retinal Biochip, 'Close examination')
Automated message after solving silo globe game.
AI Chip: Hint #1 (when in claw control room after solving globe game)
AI Chip: Hint #2 (when in claw control room after solving globe game)
Automated message after dealing with robot (doesn't matter which way you choose).

Head to the crowbar door.
Automated message after opening door, only WITH the Shield biochip.
Leave and complete Mars.

Head to the reactor door.
AI Chip: Hint #1 (once you open the reactor door WITH Shield Biochip, before stepping inside)
AI Chip: Environ Scan (reactor room)
AI Chip: Hint #1 (facing reactor lock puzzle, BEFORE using Nitrogen/crowbar)
AI Chip: Hint #2 (facing reactor lock puzzle, BEFORE using Nitrogen/crowbar)
AI Chip: Hint #3 (facing reactor lock puzzle, BEFORE using Nitrogen/crowbar)
Automatic message when picking up the card bomb.
Automatic message when facing the Airlock ('low oxygen beyond this point')
SAVE FIRST: Inside maze with oxygen ON, low OXYGEN warning (50%) (15 minutes)
Inside maze with oxygen ON, low OXYGEN warning (25%) (22.5 minutes)
Inside maze with oxygen ON, low OXYGEN warning (5%) (28.5 minutes) (Load save)
Do not destroy enemy ship, use tractor beam (1 gravcannon, 4 damping beams, 1 tractor beam).
Automated message when transporting to enemy ship.

AI Chip: Mission Briefing

AI Chip: Mission Briefing
AI Chip: Hint #1 (facing roof door BEFORE inserting Card Bomb, 'Examination of inventory/biochips')
Do not put on Shield Biochip yet.
AI Chip: Hint #1 (facing roof door AFTER inserting Card Bomb but BEFORE explosion)
AI Chip: Hint #2 (facing roof door AFTER inserting Card Bomb but BEFORE explosion)
AI Chip: Hint #3 (facing roof door AFTER inserting Card Bomb but BEFORE explosion)
Now put on Shield Biochip. You might die a couple times if you are slow, Just hit Continue.
Automated message once you step outside.
AI Chip: Hint #1 (once you step outside)
AI Chip: Environ Scan (outside on roof)
Use the stun gun on Sinclair ('bomb detonation is imminent')
AI Chip: Hint #1 (two squares before the bomb in either direction, 'detecting buildup')
AI Chip: Hint #1 (when solving bomb puzzle)
AI Chip: Hint #2 (when solving bomb puzzle)