Episode Shuttle Lost 

Passengers Aboard Shuttle

How Shuttle Lost

"Initiations"

Chakotay

Chakotay's shuttle is destroyed as he escapes a Kazon ship

"Non Sequitur"

The Shuttlecraft Drake

Harry

As Harry returns from the alternate reality on Earth, his shuttle is destroyed from a warp core breach. 

"Parturition"

Both Neelix and Paris

As they journey to planet hell to obtain supplies, the shuttle crash lands after atmospheric turbulance.

"Coda"

The Shuttlecraft Sacajewa

Janeway and Chakotay

Janeway and Chakotay crash land many times in this episode

"Unity"

Chakotay and an officer

Shuttle landed, but was raided by former Borg

"Rise"

Neelix and Tuvok, plus the Nezu Representatives

The Shuttle crashes as it is trying to investigate a series of asteroid showers on the planet.

"The Gift"

Kes

Although not destroyed, Kes brought it with her as she travelled to the other state of being.

"Day of Honour"

The Shuttlecraft Cochrane

Paris and Torres

As they try to retrieve the ejected warp core, they are attacked by the Cataati, thus causing a warp core breach.

"Nemesis"

Chakotay

Crash lands on the planet on a routine sensor sweep of the planet

"Hunters"

Seven and Tuvok

Shuttle captured by the Hirogen while Tuvok and Seven were attempting to repair a Communications Array/Network

"Drone"

Torres, Doctor, Paris, Seven

Shuttle destroyed while exploring an expanding nebula.

"Counterpoint"

Telepathic Aliens

Two shuttles were given to a species of telepathic aliens who were attempting to escape persecution by the Devore Imperium.

"Gravity"

Doctor, Tuvok, Paris

The shuttle gets caught in a gravity sinkhole and crash on a deserted planet.

"Dark Frontier"

None

An empty shuttle is used to distract the Borg so they can lower their shields, thus allowing the away team to transport aboard the sphere.