| Chapter 1: New Arrivals | Using Stasis on the malfunctioning door below the Tram Control Room before Daniels's call. | Log: Stasis Door |
| Chapter 1: New Arrivals | Attaching the right claw in the Tram Repair Room with Stasis before Daniels's call. | Log: Autoloader |
| Chapter 4: Obliteration Imminent | Damaging or killing the first Brute in the Main Atrium before Hammond's call. | Log: Shoot It In the Back |
| Chapter 4: Obliteration Imminent | Switching the last of the three power breakers. If Mining Administration or Electrical Systems is still left, its log never plays this run. Rerouting Mining Administration first, Electrical Systems second and Water Purification last keeps both logs. | Log: Mining Admin Rerouted, Log: Watch the Outlets |
| Chapter 6: Environmental Hazard | Walking into Food Storage through the Central Hub's east airlock. If the Enzyme was not crafted first, "Go to Food Storage" can no longer play in this run. | Log: Go to Food Storage |
| Chapter 6: Environmental Hazard | Injecting Wheezer 01 in West Seedling Room B. If it was not shot first, "Use the Enzyme" can no longer play in this run. | Log: Use the Enzyme |
| Chapter 7: Into the Void | Starting "You Are Not Authorized" any other way before trying the Tools Storage door: using the Captain's Nest's Bridge Security console (from Chapter 4), or, by one report, picking up a crew RIG first. The call then never plays in this run, and New Game+ begins with the Master Override, so it can't play there either. | Log: Custom Lockdown (starts You Are Not Authorized) |
| Chapter 9: Dead on Arrival | Taking the Valor's Singularity Core, which starts the escape; the Valor is lost for good once you go out through its airlock. | Log: Orders, Log: Alien Boarders, Schematic: Large Med Pack, Front Toward Enemy: survive the Shooting Range, Power Node: Valor airlock wall, Power Node: Shooting Range locker, Power Node: Brute in Valor Cargo Bay, Power Node: Valor Engine Room past the fire, Save: Valor airlock room, Save: outside the Torpedo Bay, Save: Valor Armory, Save: before the Valor Engine Room |
| Chapter 11: Alternate Solutions | Accepting the boarding prompt at the shuttle in the Main Hangar Bay. The Ishimura is closed for the rest of this run; anything still left on the ship has to wait for New Game+. | nothing flagged (last-chance checklist above it) |
| Chapter 12: Dead Space | Following the Marker through the opened shutter into the Supply Depot, where a quarantine seals you in. The strictest reading is that the landing pad area can't be revisited for its pickups after that. | Power Node: Main Landing Pad, Power Node: Landing Pad Atrium, Log: They Left Us |
| Chapter 12: Dead Space | The Marker reaching the Transfer Junction. Under the strictest reading, the Supply Depot and its Holding Zones are gone for this run after that. | Power Node: Holding Zone 2B |
| Chapter 12: Dead Space | Following the Marker out of the Transfer Junction into the Storage Chamber. Under the strictest reading, the junction's pickups can't be reached again in this run. | Power Nodes: Transfer Junction Master Override chest, Power Node: Brute in Transfer Junction |
| Chapter 12: Dead Space | Using the last terminal, where the balconies end, which plays the pedestal cutscene. Under the strictest reading, the Excavation Site's platforms are closed to you after it. | Log: Recombination Study |
| Chapter 12: Dead Space | Walking out onto the Main Landing Pad toward the shuttle, which starts the final fight. The storage room's Node and anything left in the Living Quarters are lost for this run after that. | Log: Retrieval Order, Power Node: past the Access Tunnel |
| New Game+: Chapters 1–5 (Plasma Cutter only) | Finishing the Mining Administration or Electrical Systems reroute before Water Purification's. Rerouting Water Purification first, then the other two in either order, keeps its log safe. | Log: Water Purification |
| New Game+: Chapters 6–10 | Crafting the Enzyme at the Central Hub terminal before walking into Food Storage. Walking into Food Storage first and crafting the Enzyme afterwards keeps "Inject the Wheezers" safe. | Log: Inject the Wheezers |
| New Game+: Chapters 11–12 and the alternate ending | Accepting the boarding prompt at the shuttle in New Game+. The Ishimura is closed for the rest of the run: a fragment not yet taken, or a placement not yet made, can no longer happen, and the standard ending plays. | Marker Fragment 1: Maintenance Bay Office, Marker Fragment 2: Dr. Kyne's hidden room, Marker Fragment 3: Engine Room alcove, Marker Fragment 4: Bridge Break Room, Marker Fragment 5: Dr. Mercer's office, Marker Fragment 6: Cryogenics, on top of the chamber, Marker Fragment 7: East Grow Chamber, top balcony, Marker Fragment 8: Mineral Samples (Level 3), Marker Fragment 9: Comms Array room, Marker Fragment 10: Deluxe Shift Bunks, Marker Fragment 11: Inquiry Desks, Marker Fragment 12: Cargo Bay shelving, Place all 12 Marker Fragments on the captain's table |