The Khonshu-class shuttlecraft is equipped with similar stealth features to the larger Amun-Ra frigate. This shuttle is able to serve as a forward scout for the frigate and is capable of traveling impressively long distances from its mothership to transfer personnel or supplies. The craft is kept in a concealed compartment, nearly indistinguishable from the rest of the frigate's hull, and can be quickly deployed as an evacuation craft in the event of an emergency.
Following the Protomolecule outbreak on the Anubis, the lone survivor, Julie Mao, took the shuttle to Eros Station, waiting for an OPA rescue. However, she was exposed to the Protomolecule at some time, and died aboard Eros, allowing for the start of the Eros Incident. The Anubis shuttle likely remained there until Eros's crash into Venus.
Hot on Julie's trail, Miller arrived at Eros to find that the ship that had docked at Eros was not the Anubis itself, but its shuttle Anubis-1A, registered to a "Lionel Polanski." However, his aggressive means of obtaining this information from Eros' dock master nearly landed him in jail.
Another Khonsu class shuttle was used to transport Jules-Pierre Mao to Prospero Station on Io, presumably from the Guanshiyin, where he had just left to allow for the Attempted UN asassination of Chrisjen Avasarala.
- In Egyptian Mythology, Khonsu was the God of the Moon, in keeping with Protogen's theme of Egyptian named ships.
- Khonsu is also the child of Amun in Egyptian Mythology, giving the class an appropriate name; being a "child" ship to an Amun-Ra class ship