The Augment missions are the Khan storyline in Star Trek Fleet Command, 45 missions that follow Khan Noonien Singh and his Augments through the Vaara Expanse, from the first distress call in Uncaged to Khan turning his forces on the Federation in The Coming Darkness. Only the Augments Exodus chain carries a recommended level, 28; the rest have none, and the warp needed to complete a mission runs from 1 to 23. The headline rewards are officer shards for Joaquin, Khan, John Harrison, Otto, Marla McGivers and Kati, large stacks of Ultra and Premium Recruit Tokens, Dark Matter and Augment Points.
How the Augment missions work
The main Augments storyline is a numbered run of single missions that climbs in warp as it goes. Ungehemmt opens it at warp 13, and early parts such as Der Müll eines Mannes, Außenbezirke und Wir sind besser stay at warp 7 to 13. The later parts need warp 21 to 23: The Die is Thrown at 21, then Rückläufiges Licht und The Coming Darkness at 23. Between them sit collection steps at warp 1 that send you nowhere. Flüchtige Kombinationen und Erholung each ask you to collect 3 Dark Matter samples from missions in the region, while No Rest for the Wicked und Das Auge des Sturms ask for 500 and 700 Augment Credits.
Several missions end on a choice that decides the reward. Eine verlässliche Quelle pays Khan shards if you lie to the Tal Shiar agent, Eine Grenze überschreiten pays them if you attack the Klingons, and Die andere Seite pays them if you bombard the colony on Thomax. The Coming Darkness splits between helping Khan attack the Federation and betraying him to Starfleet.
The three Autopilot missions are one-step donations. Autopilot: Yarda, Autopilot: Duriana und Autopilot: Tera Lara each ask you to give Khan 3,000 Dilithium for his experimental warp technology, need warp 7, and have no combat. Yarda pays the 3,000 Dilithium straight back, Duriana pays 100,000 Parsteel and Tera Lara pays 18,000 Tritanium.
Two chains run alongside the story. Botany Bay is eight warp 1 parts, each asking you to gather Common, Uncommon or Rare Plutonium to tier up the Botany Bay. Erweitert Exodus is the level 28 chain in which Otto and Kati search for their lost Augment brothers, Rima and Pan, with warp from 7 to 22 and fights of around 130,000 strength.
Augment mission rewards worth chasing
Joaquin is the easiest officer to collect here. The Botany Bay chain pays 84 Joaquin shards across its eight parts, rising from 3 in Part 1 to 22 in Part 8, and Nachrüstung pays 14 more at warp 10. Khan Noonien Singh shards come from four missions: 4 each from the Khan-side paths of A Reliable Source, Crossing A Line and The Other Side, and 8 from helping Khan in The Coming Darkness. Ungehemmt pays 6 John Harrison shards and Irreführung pays 7, Lehren aus der Vergangenheit pays 7 Marla McGivers shards, and Augments Exodus pays 4 Otto shards and 4 Kati shards across its parts.
Betraying Khan in The Coming Darkness pays 1,600 Ultra Recruit Tokens, the largest token payout here, Unter der Ferse pays 1,200, and Eye of the Storm pays 800 Ultra with 450 Premium for nothing more than 700 Augment Credits. Recuperation adds 600 Premium Recruit Tokens and Volatile Combinations 800 Ultra. For Augment Points, The Coming Darkness pays 2,000 on either path and Eye of the Storm pays 1,250.
Augment mission chains
- Botany Bay: 8 parts, no recommended level, warp 1 throughout.
- Erweitert Exodus: 5 missions, level 28, warp 7 to 22 to complete. Parts 2 to 5 are covered on the Augments Exodus Parts 2 to 5 page.
All 45 Augment missions
The table lists every Augment mission sorted by recommended level, which puts the level 28 Augments Exodus chain last; Botany Bay links go straight to that part’s section on the chain page.
| Mission | Ebene | Warp to complete | Belohnungen |
|---|---|---|---|
| A Calculated Risk | 21 | 3 1 Day Speed Up, 19 3 Hour Speed Up, 1 Dark Matter, 100 Augment Points | |
| Eine verlässliche Quelle | 21 | 4 Khan Noonien Singh shards, 9 3★ Uncommon Refined Ore, 10 3 Hour Speed Up, 1 Dark Matter | |
| Autopilot: Duriana | 7 | 100K Parsteel | |
| Autopilot: Tera Lara | 7 | 18K Tritanium | |
| Autopilot: Yarda | 7 | 3.000 Dilithium | |
| Unter der Ferse | 17 | 1,200 Ultra Recruit Token, 1 Dark Matter, 70 Augment Points | |
| Botany Bay Teil 1 | 1 | 3 Joaquin shards | |
| Botany Bay Teil 2 | 1 | 3 Joaquin shards, 11 1 Hour Speed Up | |
| Botany Bay Teil 3 | 1 | 5 Joaquin shards, 4 3 Hour Speed Up | |
| Botany Bay Teil 4 | 1 | 7 Joaquin shards, 6 3 Hour Speed Up | |
| Botany Bay Teil 5 | 1 | 10 Joaquin shards, 8 3 Hour Speed Up | |
| Botany Bay Teil 6 | 1 | 16 Joaquin shards, 10 3 Hour Speed Up | |
| Botany Bay Teil 7 | 1 | 18 Joaquin shards, 5 8 Hour Speed Up | |
| Botany Bay Teil 8 | 1 | 22 Joaquin shards, 6 8 Hour Speed Up | |
| Gebrochene Ketten | 12 | 6 Klingon Recruit Token, 48K Parsteel, 9 1 Hour Speed Up, 7,000 Tritanium | |
| Die Reue des Käufers | 12 | 6 Klingon Recruit Token, 18 2★ Uncommon Refined Crystal, 43K Parsteel, 160 2★ Survey Parts | |
| Eine Grenze überschreiten | 21 | 4 Khan Noonien Singh shards, 13 3★ Uncommon Refined Crystal, 500 Klingon Recruit Token, 34K Dilithium | |
| Gleicher Anteil | 12 | 6 Klingon Recruit Token, 12 2★ Uncommon Refined Ore, 700 Dilithium | |
| Das Auge des Sturms | 1 | 800 Ultra Recruit Token, 450 Premium Recruit Token, 41K Dilithium, 1,250 Augment Points | |
| Lehren aus der Vergangenheit | 13 | 7 Marla McGivers shards, 600 Dilithium, 18 15 Minute Speed Up, 40 Augment Points | |
| Geist über Materie | 13 | 904K Parsteel, 13 3★ Uncommon Refined Ore, 1 Dark Matter, 40 Augment Points | |
| Irreführung | 11 | 7 John Harrison shards, 2,700 Tritanium, 19 15 Minute Speed Up | |
| No Rest for the Wicked | 1 | 1 3★ Rare Refined Crystal, 1 3★ Rare Refined Gas, 1 3★ Rare Refined Ore, 300 Augment Points | |
| Die Reklametafel | 17 | 23K Dilithium, 33 15 Minute Repair Speed Up, 1 Dark Matter, 30 Augment Points | |
| Der Müll eines Mannes | 13 | 25 2★ Uncommon Refined Ore, 38K Parsteel, 160 2★ Battleship Parts | |
| Außenbezirke | 13 | 8 3 Hour Speed Up, 36 5 Minute Repair Speed Up, 70 Augment Points | |
| Outsourcing | 17 | 12 3★ Uncommon Refined Ore, 12 3★ Uncommon Refined Gas, 12 3★ Uncommon Refined Crystal, 1 Dark Matter | |
| Quid Pro Quo | 13 | 6 Klingon Recruit Token, 20 2★ Uncommon Refined Crystal, 140 2★ Survey Parts, 30 15 Minute Speed Up | |
| Rückläufiges Licht | 23 | 752K Parsteel, 7 3 Hour Speed Up | |
| Erholung | 1 | 37K Tritanium, 600 Premium Recruit Token | |
| Nachrüstung | 10 | 14 Joaquin shards | |
| Wiedersehen | 12 | 6 Klingon Recruit Token, 15 2★ Uncommon Refined Ore, 240 2★ Battleship Parts, 5,000 Tritanium | |
| Nachhaltigkeit | 21 | 2 3★ Rare Refined Crystal, 2 3★ Rare Refined Gas, 2 3★ Rare Refined Ore, 1 Dark Matter | |
| The Coming Darkness | 23 | 8 Khan Noonien Singh shards, 15 3 Hour Speed Up, 2.8M Parsteel, 418K Tritanium | |
| The Die is Thrown | 21 | 31K Dilithium, 200 Augment Points, 821K Parsteel, 5 8 Hour Speed Up | |
| Die andere Seite | 21 | 4 Khan Noonien Singh shards, 821K Parsteel, 1 Dark Matter, 100 Augment Points | |
| Das Gespenst von Terazon X31 | 21 | 12 3★ Uncommon Refined Gas, 12 3★ Uncommon Refined Crystal, 400 Ultra Recruit Token | |
| Ungehemmt | 13 | 6 John Harrison shards, 1,500 Dilithium, 32 5 Minute Repair Speed Up | |
| Flüchtige Kombinationen | 1 | 800 Ultra Recruit Token | |
| Wir sind besser | 7 | 53K Tritanium, 11K Dilithium, 90 Augment Points | |
| Erweitert Exodus | 28 | 22 | 2 Otto shards, 213K Tritanium |
| Erweiterungen Exodus Teil 2 | 28 | 15 | 100 Augment Credits, 400 Corrupted Data |
| Erweiterungen Exodus Teil 3 | 28 | 15 | 4 Kati shards, 2 Otto shards |
| Erweiterungen Exodus Teil 4 | 28 | 19 | 50 Augment Credits, 14 3★ Uncommon Refined Gas, 400 Corrupted Data, 33 Common Plutonium |
| Erweiterungen Exodus Teil 5 | 28 | 7 | 85K Tritanium, 15 1 Hour Speed Up, 11 15 Minute Repair Speed Up |
Die Swarm missions und die Separatists missions are the other storylines without level recommendations, both in a similar warp range. For every mission in the game sorted by level, use the mission guide.


