Augment Missions

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. Uncaged opens it at warp 13, and early parts such as One Man’s Trash, Outskirts and We Are Better stay at warp 7 to 13. The later parts need warp 21 to 23: The Die is Thrown at 21, then Receding Light and The Coming Darkness at 23. Between them sit collection steps at warp 1 that send you nowhere. Volatile Combinations and Recuperation each ask you to collect 3 Dark Matter samples from missions in the region, while No Rest for the Wicked and Eye of the Storm ask for 500 and 700 Augment Credits.

Several missions end on a choice that decides the reward. A Reliable Source pays Khan shards if you lie to the Tal Shiar agent, Crossing A Line pays them if you attack the Klingons, and The Other Side 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 and 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. Augments 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 Retrofit 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. Uncaged pays 6 John Harrison shards and Misdirection pays 7, Lessons of the Past 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, Beneath the Heel 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.
• Augments 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.

The Swarm missions and the 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.