There are many types of missions in Shelter 69. Some require specific Champions and some may have any Champions assigned to them. Each follows the same process of exploring a map with the mission team, potentially encountering enemies, finding loot, or engaging in dialogue. Once the mission is completed, assuming the Champion is not unconscious, they immediately return to whatever task you had previously assigned them to. If any Champions are knocked unconscious, they must be treated in the Medbay and then reassigned to their previous job.
¶ Campaign Missions
These missions make up the main storyline for Shelter 69. Completing specific missions is required to upgrade your Shelter Level. They can be replayed repeatedly to see the story again, and to collect loot from the missions. Along with loot, some missions also unlock new Champions and H-scenes relevant to the main storyline.
These missions are also the only ones which use a star system - if you complete the mission without any Champions being knocked unconscious, you get 3 stars. Each Champion lost reduces the number of stars by 1. Collecting stars awards extra rewards from the Campaign Chapter - resources and crates. Unlocking the next Campaign Chapter requires completing all of the missions in the current chapter, plus getting three stars on most of the missions.
¶ Farming Campaign Missions
Campaign missions can be run over and over for additional loot, including flirt items, equipment and nanites. Some of the more popular stages for this at the moment are 2-1, 2-2, 3-9, 4-4, and 4-5.
¶ Champion Missions
Champion Missions are narrative missions related to a specific Champion. In the case of Crate Champions, the Champion Mission tells the story of how they joined the Shelter, and you must complete the mission in order to have the Champion join your shelter. For Campaign Champions, these missions are unlocked once you reach a certain point in the Campaign, after they have joined your shelter. Champion Missions can only be played once, and are a key part of the Champion's story.
If you've forgotten what occurred in a Champion's Mission, you can find summaries of them here. Be warned - some may be heavy on the spoilers.
¶ Resource Missions
Resource Missions can be run repeatedly in order to collect resources (credits, stone, and metal), along with the possibility of some additional loot. Each time you unlock a new Campaign Chapter, you also unlock the first Resource Mission for that chapter. To unlock the rest of the Resource Missions for each chapter, you need to complete the Resource Missions for that chapter in order (e.g. you need to complete Mission 4 to unlock Mission 5, but Mission 6 unlocks as soon as you unlock Campaign Chapter 2). So far each Chapter has included five Resource Missions.
Reward amounts listed in the table are based on the amount listed in game, but those are just the average numbers. Each time you run a mission your real reward will vary slightly (between -10% to +20%) from the amount offered. They also do not include the possibility of more resources from chests during the mission.
¶ Loot Drops
Some Resource Missions can also provide additional loot from chests in the mission or bonus loot on completion. The kind of loot available during a Resource Mission appears to be determined by the loot table used for that mission. There seem to be three types of loot tables.
| Loot Table | Possible Drops1 |
| Treasure | Nanites, Training Materials, Flirt Items, Enhancement Gems, Chrome Readjusters, Crafting Materials |
| Equipment | Weapons, Clothing, and Trinkets |
| Resources | Credits, Stone, and Metal |
1All loot tables can also drop eLDi.
¶ Missions
| Chapter 1 | ||||||||
| Name | CR | Enemies | Loot Drops | Avg. Coins | Avg. Stone | Avg. Metal | Duration | |
| 1 | Salvaging Credits | 40 | 5 | - | 108 | 0 | 0 | 7 |
| 2 | Looking For Funds | 50 | 6 | - | 150 | 0 | 0 | 7 |
| 3 | Making Money | 60 | 7 | - | 173 | 0 | 0 | 13 |
| 4 | Digging For Credits | 70 | 5 | - | 221 | 0 | 0 | 10 |
| 5 | Quick Raids | 85 | 7 | - | 209 | 81 | 0 | 10 |
| Chapter 2 | ||||||||
| Name | CR | Enemies | Loot Drops | Avg. Coins | Avg. Stone | Avg. Metal | Duration | |
| 6 | Securing Small Haul | 110 | 4 | Treasure 5-10 credits |
270 | 108 | 0 | 10 |
| 7 | Foraging For Supplies | 120 | 8 | Resource | 310 | 119 | 98 | 10 |
| 8 | Doing Minor Favors | 130 | 6 | 1-3 eLDi | 389 | 165 | 134 | 10 |
| 9 | Raiding Enemy Outpost | 150 | 6 | - | 442 | 213 | 185 | 6 |
| 10 | Spoils Of War | 180 | 9 | Treasure | 469 | 260 | 222 | 9 |
| Chapter 3 | ||||||||
| Name | CR | Enemies | Loot Drops | Avg. Coins | Avg. Stone | Avg. Metal | Duration | |
| 11 | Quick Run | 200 | 7 | - | 545 | 426 | 290 | 8 |
| 12 | Recovering Resources | 220 | 9 | Resource | 560 | 634 | 408 | 12 |
| 13 | Securing Medium Haul | 245 | 5 | Equipment | 748 | 610 | 610 | 11 |
| 14 | Searching Old Depots | 255 | 7 | - | 760 | 712 | 587 | 6 |
| 15 | Raiding Requisition Center | 290 | 7 | Treasure | 876 | 700 | 679 | 10 |
| Chapter 4 | ||||||||
| Name | CR | Enemies | Loot Drops | Avg. Coins | Avg. Stone | Avg. Metal | Duration | |
| 16 | Quick Reconnaissance | 320 | 11 | - | 997 | 823 | 749 | 18 |
| 17 | Resource Raid | 340 | 14 | Resource1 | 978 | 994 | 751 | 11 |
| 18 | Recovering Supplies | 360 | 11 | Resource1 | 1124 | 993 | 948 | 10 |
| 19 | Raiding Enemy Outpost | 380 | 6 | Equipment1 | 1133 | 1123 | 957 | 7 |
| 20 | Liberating Enemy Assets | 400 | 6 | Resource | 1206 | 1171 | 1091 | 7 |
| Chapter 5 | ||||||||
| Name | CR | Enemies | Loot Drops | Avg. Coins | Avg. Stone | Avg. Metal | Duration | |
| 21 | Supply Run | 420 | 9 | Resource | 1396 | 1233 | 1218 | 17 |
| 22 | Resources Takeover | 440 | 6 | Equipment | 1459 | 1332 | 1204 | 14 |
| 23 | Doing Major Favors | 460 | 7 | Resource | 1590 | 1520 | 1388 | 11 |
| 24 | Securing Great Haul | 480 | 6 | - | 1790 | 1573 | 1549 | 10 |
| 25 | Clearing Enemy Forts | 490 | 10 | - | 1717 | 1695 | 1543 | 11 |
| Chapter 6 | ||||||||
| Name | CR | Enemies | Loot Drops | Avg. Coins | Avg. Stone | Avg. Metal | Duration | |
| 26 | Deeper Underground | 500 | 4 | Equipment Resource |
1883 | 1743 | 1624 | 19 |
| 27 | Deserted Outpost | 525 | 7 | Resource x2 | 2015 | 1813 | 1781 | 19 |
| 28 | Get Schooled | 550 | 12 | Resource x2 Equipment |
2165 | 1963 | 1866 | 16 |
| 29 | Sandy Shacks | 575 | 10 | Resource x2 | 2272 | 2162 | 1989 | 24 |
| 30 | Sine Field | 600 | 8 | Resource x2 Equipment |
2364 | 2248 | 2128 | 26 |
| Chapter 7 | ||||||||
| Name | CR | Enemies | Loot Drops | Avg. Coins | Avg. Stone | Avg. Metal | Duration | |
| 31 | Abandoned Outpost | 620 | 9 | Resource x3 Equipment Treasure |
2468 | 2308 | 2348 | 21 |
| 32 | House of Wares | 640 | 10 | Resource x3 Equipment |
2660 | 2585 | 2493 | 22 |
| 33 | Desert Tower | 660 | 9 | Resource x31 Equipment Treasure |
2835 | 2758 | 2671 | 17 |
| 34 | Abandoned Shacks | 680 | 10 | Resource x31 Equipment Treasure x2 |
3122 | 2885 | 2852 | 21 |
| 35 | The Slammer | 700 | 13 | Resource x31 Equipment Treasure |
3151 | 3087 | 3094 | 20 |
| Chapter 8 | ||||||||
| Name | CR | Enemies | Loot Drops | Avg. Coins | Avg. Stone | Avg. Metal | Duration | |
| 36 | Old Military Base | 720 | 29 | Resource x3 | 3492 | 3381 | 3227 | |
| 37 | Small Fort | 740 | 25 | Resource x2 Treasure |
3667 | 3468 | 3227 | |
| 38 | R&D Facility | 760 | - | Resource x4 Treasure |
3735 | 3775 | 3538 | |
| 39 | Infested Trove | 780 | 25-28 | Resource x3 Treasure |
3931 | 3886 | 3809 | |
| 40 | Desert Quod | 800 | - | Resource x2 Equipment Treasure |
4141 | 4184 | 3953 | |
| Chapter 9 | ||||||||
| Name | CR | Enemies | Loot Drops | Avg. Coins | Avg. Stone | Avg. Metal | Duration | |
| 41 | Shopping Time! | 820 | 4320 | 4381 | 4280 | |||
| 42 | Frosty Lab | 840 | 4543 | 4551 | 4417 | |||
| 43 | Sex Machines Warehouse | 860 | 4793 | 4782 | 4544 | |||
| 44 | Tag! You're It! | 880 | 4941 | 4873 | 4755 | |||
| 45 | Pain's Old Stash House. | 920 | 5257 | 5092 | 5086 | |||
1These missions give some loot drops as a bonus reward upon completion, they are not all collected mid-mission.
Loot quantities per drop are roughly:
Equipment: 1
Intel: 10 - 15
eLDi and Gloves: 1 - 4
Enhance Material(Sapphire, Amethyst): 1 - 4
Chrome Readjuster: 3 - 4
Flirt Items: 1 - 2
Duration is:
Small Room: 1
Large Room: 2
Elevator: 3
So Resource 2 is: 2 Small, 1 Large, 1 Elevator = 7
¶ Secret Locations
These are difficult solo missions found during expeditions that have a chance to provide excellent loot - particularly nanites and enhancement gems. Finding them is fairly random, though they have a higher chance to be found in longer expeditions.
The list of Missions below is incomplete - a lot of new Secret Locations have been added and it seems likely that which Secret Locations your Champions can find is based on your Shelter Level or Expedition Level - so not all Secret Locations are available to everyone.
| Secret Location | Power | Enemies | Loot Drops1 |
| Desert Mine | 50 | 4 | Treasure x1 Resource x1 |
| Smoke on the Top | 400 | 9 | Treasure x5 |
| Old House | 500 | 5 | Equipment x1 Unknown Resource x1 |
| Abandoned Houses | 550 | 7 | Treasure x3 |
| Makeshift Bunker | 600 | 6 | Treasure x3 |
| Desert Outpost | 750 | 6 | Treasure x2 |
| Tamer's Den | 750 | 8 | Treasure x3 |
| Lunatic Asylum | 1000 | 4 | Treasure x2 |
| Maximum Security | 1000 | 10 | Treasure x4 |
| Weapons Factory | 1250 | 6 | Treasure x3 |
| Desert Oasis | 1750 | 9 | Treasure x3 Equipment x1 |
| Desert Asylum | 1750 | 10 | Treasure x2 Resource x1 |
| Deserted Radio Station | 2600 | 10 | Treasure x3 Resource x1 |
| Dildo Factory | 2800 | 10 | Treasure x2 Resource x1 Equipment x1 |
1These missions give some loot drops as a bonus reward upon completion, they are not all collected mid-mission.
¶ Trust Missions
These missions allow you to earn Trust for a specific Champion, and while they do not contain dialogue each mission description explains what you are doing to help build Trust with the Champion. These missions require Trust Tokens.