The Caduceus was a Zion hovercraft.
After the Crisis Meeting, Ballard offered to help Morpheus and remain behind and wait for contact from the Oracle. While receiving her message, the crew member Bane was attacked by Smith, who overwrote his mind.
During the defense of Zion, Bane/Smith killed the entire crew and used the ship's EMP to disable at least five ships (including itself, the Icarus, the Gnosis, and the Novalis). Bane was the only survivor and was saved by the Mjolnir.
Name
The name of the Caduceus comes from the Greek word "caduceus", which is the symbol of two snakes wrapped around a winged staff, commonly used as a medical symbol.