For PvE

Generic Crews (51 and below)

Vs Energy Weapon Hostiles

Vs Kinetic Weapon Hostiles

(c) Cadet Uhura (Another Time) - Cadet McCoy (Another Time) - Common T'Laan (Starfleet Academy) / Rare Cath (Ferengi Conglomerate)
(c) Next Gen La Forge (NextGen) - Next Gen Crusher (NextGen) - Rare Cath (Ferengi Conglomerate)
(c) Epic Chrisopther Pike (Shakedown Cruise) - Rare Moreau (Shakedown Cruise) - Common T'Laan (Starfleet Academy) / Rare Cath (Ferengi Conglomerate)
(c) Epic Jean-Luc Picard (TNG Crew) - Rare Beverly Crusher (TNG Crew) - Rare Cath (Ferengi Conglomerate)

Specific Crews

SNW Crew

(c) Epic SNW Pike (Strange New Worlds) - any SNW officer for synergy - swap officer based on opponent ship type
Rare SNW Ortegas (Strange New Worlds) - Vs Explorers when using a Battleship
Rare SNW Spock (Strange New Worlds) - Vs Interceptors when using an Explorer
Rare SNW Nyota Uhura (Strange New Worlds) Vs Battleships when using an Interceptor

Vs Borg Probes

Preferred Ship: Vidar or Vi'dar Talios
Alternative Ship: Any Interceptor
Lower Ops

(c) Epic Chrisopther Pike (Shakedown Cruise) - Rare Moreau (Shakedown Cruise) - Common T'Laan (Starfleet Academy) / Rare Cath (Ferengi Conglomerate)
(c) Rare Seven of Eleven (Unimatrix Twelve) - Uncommon Eight of Eleven (Unimatrix Twelve) - Uncommon Nine of Eleven (Unimatrix Twelve)

Higher Ops

(c) Epic Five Of Eleven (Unimatrix Twelve) - Uncommon Eight of Eleven (Unimatrix Twelve) - Uncommon Nine of Eleven (Unimatrix Twelve)
(c) Epic SNW Pike (Strange New Worlds) - Rare SNW Nyota Uhura (Strange New Worlds) - any SNW officer for synergy

Vs up to Level 35 Swarm Hostiles

Preferred Ship: Franklin
Alternative Ship: Any Explorer
Crew:

(c) Epic Chrisopther Pike (Shakedown Cruise) - Rare Moreau (Shakedown Cruise) - Common T'Laan (Starfleet Academy) / Rare Cath (Ferengi Conglomerate)
(c) Epic SNW Pike (Strange New Worlds) - Rare SNW Spock (Strange New Worlds) - any SNW officer for synergy

Vs Level 37+ Swarm Hostiles

Preferred Ship: USS Franklin or USS Franklin-A
Alternative Ship: Any Explorer

(c) Epic SNW Pike (Strange New Worlds) - Rare SNW Spock (Strange New Worlds) - any SNW officer for synergy
(c) Epic SNW Pike (Strange New Worlds) - Rare SNW Spock (Strange New Worlds) - Epic Jaylah
(c) Epic Chrisopther Pike (Shakedown Cruise) - Rare Moreau (Shakedown Cruise) - Common T'Laan (Starfleet Academy) / Uncommon Chen (Starfleet Academy) / Rare Cath (Ferengi Conglomerate)

Vs Eclipse Hostiles

Preferred Ship: Stella
Alternative Ship: Any
Crew: Generic vs Energy/Kinetic Weapon Crew

(c) Epic Chrisopther Pike (Shakedown Cruise) - Rare Moreau (Shakedown Cruise) - Common T'Laan (Starfleet Academy) / Uncommon Chen (Starfleet Academy)
(c) Epic Eurydice (Mudd's Company) - Epic Mudd (Mudd's Company) - Common Tiza (Mudd's Company)

Vs FKR hostiles

Preferred ship: Any
(Generic Crews work as well as the SNW crew)

Vs Federation Hostiles

(c) Epic Kang (Blood & Honor) - Rare Krell (Blood & Honor) - Uncommon - Rare Mara (Blood & Honor) / Uncommon Linkasa (Blood & Honor)
(c) Epic Liviana Charvanek (Romulan Patriots) - Rare Mirek (Romulan Patriots) - Rare Tal (Romulan Patriots) / Uncommon D'jaoki (Romulan Patriots)
(c) Epic Jean-Luc Picard (TNG Crew) - Epic William T. Riker (TNG Crew) - Rare Beverly Crusher (TNG Crew)

Vs Klingon Hostiles

(c) Liviana Charvanek (Romulan Patriots) - Uncommon L'nar (Romulan Patriots) - Rare Tal (Romulan Patriots) / Uncommon D'jaoki (Romulan Patriots) / Rare Tomalak (Pride of Romulus)
(c) Epic Jean-Luc Picard (TNG Crew) - Epic Geordi LaForge (TNG Crew) - Rare Beverly Crusher (TNG Crew)

Vs Romulan Hostiles

(c) Epic Kang (Blood & Honor) - Uncommon Yan'agh (Blood & Honor) - Rare Mara (Blood & Honor) / Uncommon Linkasa (Blood & Honor) / Rare Yuki Sulu (Section 31)
(c) Epic Jean-Luc Picard (TNG Crew) - Epic Deanna Troi (TNG Crew) - Rare Beverly Crusher (TNG Crew)

Vs Actian Hostiles

Preferred ship: Mantis

(c) Epic SNW Pike (Strange New Worlds) - Rare SNW Spock/Nyota Uhura/Ortegas (depending on ship type) - Epic SNW Hemmer (Strange New Worlds)
Any Generic crew + Epic SNW Hemmer (Strange New Worlds) on the bridge + Rare Ghalenar (Unimatrix Twelve) on Below Decks for increased loot

Vs Freebooter Hostiles

Preferred ship: Any
(c) Epic SNW Pike (Strange New Worlds) - Rare SNW Spock/Nyota Uhura/Ortegas (depending on ship type) - Rare Beverly Crusher (TNG Crew)
(c) Rare SNW Spock/Nyota Uhura/Ortegas (Strange New Worlds) - Epic Khan (Khan's Crew) - Epic Gorkon (Klingon Patriots)

Vs Silent Hostiles

Preferred ship: Any

(c) Epic Chrisopther Pike (Shakedown Cruise) - Rare Moreau (Shakedown Cruise) - Epic Annorax (Voyager 30th Anniversary) / Epic Phlox (Enterprise NX-01) / Epic Trip Tucker (Enteprise NX-01)
(c) (c) Liviana Charvanek (Romulan Patriots) -Uncommon Severus (Romulan Patriots) - Rare Decius (Romulan Patriots)

Vs Xindi Hostiles

Preferred ship: Any, Enteprise NX-01 for Xindi Aquatic Hostiles
Recommendation: Particle Beam Delay Ex-Borg Favor for survivability

(c) Epic Jonathan Archer (Enterpise NX-01) - Epic Trip Tucker (Enterprise NX-01) - Uncommon Chen (Starfleet Academy)
(c) Uncommon Frank Leslie (Shakedown Cruise) - Rare Moreau (Shakedown Cruise) - Epic Nero (Nero's Crew) / Epic Georgiou (Discovery Crew) / Rare Tal (Romulan Patriots) / Rare Neelix (Voyager) on Below Decks

Vs Gorn Hostiles

Preferred ship: Gorn Eviscerator

(c) Epic Kathryn Janeway (Voyager) - Epic Enterprise-E Picard (Enterpise-E) - Rare Enterprise-E Data (Enterprise-E)
wok saavik
snw nurse chapel

Vs Mirror Universe Hostiles

Preferred ship: NSEA Protector

(c) Epic SNW Pike (Strange New Worlds) - Rare SNW Spock/Nyota Uhura/Ortegas (depending on ship type) - Epic SNW Una (Strange New Worlds)
(c) Epic SNW James Kirk (Strange New Worlds) - Epic SNW Sam Kirk (Strange New Worlds) - Epic SNW Una (Strange New Worlds)

Other officers to consider:

Rare Rima (Khan's Crew) - increased critical hit chance while affected by Hull Breach (all MU hostiles inflict Hull Breach)
Rare Vemet (Nero's Crew) - survivability to head back to extraction point in case your ship gets destroyed (loot is lost if ship id destroyed in MU systems)

Vs Assimilated El-Aurian Ships

Preferred ship: Any

Vs Augment Exile Hostiles (Hijacked Ships)

Preferred ship: USS Reliant (a must for Hijacked D7 and DY class ships)

(c) Epic Chrisopther Pike (Shakedown Cruise) - Rare Moreau (Shakedown Cruise) - Epic Jason Nesmith (Galaxy Quest) / Epic Annorax (Voyager 30th Anniversary)
(c) Epic Jean-Luc Picard (TNG Crew) - Rare Beverly Crusher (TNG Crew) - Epic Jason Nesmith (Galaxy Quest) / Epic Annorax (Voyager 30th Anniversary)

Other officers to consider:

Epic Dajash Tolra (Symbiosis) - increased loot from Armadas and hostiles, Captain Maneuver
Epic Enterprise-E Picard (Enteprise-E) - increased loot from Armadas and hostiles, Captain Maneuver
Rare Rachel Garrett (Enteprise-E) - increased loot from non-Armada hostiles, Officer ability
Epic Five of Eleven (Unimatrix Twelve) - increased hostiles loot, Officer ability
RareTom Paris (Voyager) - increased mitigation stats, Below Decks ability
Epic WOK Carol (Wrath of Khan) - increased shield mitigation, Below Decks ability
Rare SNW Nurse Chapel (Strange New Worlds) - increased Isolytic Cascade Damage, Below Decks ability
Epic PIC Hugh (Ex-Borg) - hull repair, Below Decks ability
Epic SNW Black Ops M'benga (Strange New Worlds) - shield health restore, Below Decks ability

Specific Crews

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