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UFP: Starfleet
Ferengi Alliance
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Klingon Empire
Romulan Star Empire
Xindi
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Star Trek Ships: Expanded - Xindi

Arboreals

Arboreal Shuttle
Abandoned on Loque'eque homeworld two weeks ago
Arboreal Ship [ 2 ]
Part of Enterprise escort
Arboreal Ship [ 5 ]
Part of 18 ship attack force
Arboreal Ship
Part of 18 ship attack force
Destroyed by anomaly

Aquatics

Aquatic Patrol [ 5+ ]
Aquatic Ship [ 4 ]
Trident
Aquatic Cruiser
Aquatic Ship
Aquatic Pod
Delivered to Enterprise
Aquatic Cruiser
Aquatic Cruiser
Presumed destroyed by anomaly
Aquatic Ship [ 5 ]
Part of 18 ship attack force
Aquatic Ship
Part of 18 ship attack force
Destroyed
Aquatic Cruiser

Insectoids

Insectoid Ship
Part of six-ship attack force
Disabled
Twelve years after new timeline formation
Insectoid Ship [ 2 ]
(simulation)
Insectoid Ship [ 100s ]
(simulation backstory)
Insectoid Hatchery Ship
Forced to land on unnamed planet due to fractured nacelle
Insectoid Shuttle
Assault vehicle aboard Hatchery ship
Taken by Enterprise
Air and water capable
Captain Archer
Retaken by Xindi
Insectoid Ship
Destroyed by Enterprise
Insectoid Ship [ 2 ]
Triaxle
Insectoid Ship [ 5 ]
Part of Xindi weapon escort
Insectoid Ship [ 5 ]
Part of Xindi weapon escort
Destroyed

Primates

Captain Degra
Taken by Enterprise
Released
Shuttle from Degra's ship
Primate Ship [ 2 ]
Part of Enterprise escort

Reptilians

Reptilian Ship [ 2 ]
(one smaller than the other)
Reptilian Shuttle
Reptilian Ship [ 2 ]
Disabled by Enterprise collision
"Several months" after new timeline formation
Reptilian Ship [ 2 ]
Probe escorts
"Several months" after new timeline formation
Reptilian Ship
Part of six-ship attack force
Twelve years after new timeline formation
Reptilian Ship
Part of six-ship attack force
Disabled
Twelve years after new timeline formation
Reptilian Ship
Destroyed by Degra
Reptilian Ship [ 10 ]
Part of Xindi weapon escort
Reptilian Ship
"Captain" Dolim
Destroyed by Kumari

Sphere Weapon

One-man Probe
Weapon testbed
Crash landed in central Asia, Earth

Other Class/Type

Garbage scow
"Weeks later" after new timeline formation

Unknown Class/Type

Ship
Raided by Osaarian pirates
Adrift for less than two days
Ship [ 2 ]
Disabled by Enterprise
Ship
Ship
Ship [ 2 ]