Under NASA's Environmental Research Aircraft and Sensor Technology (ERAST) project, NASA's Dryden Flight Research Center assisted Scaled Composites in developing a sophisticated station-keeping autopilot system and a satellite communications (SATCOM)-based uplink-downlink data system for Proteus' performance and payload data.

The Proteus wing was adapted for use on the Model 318 White Knight carrier aircraft, which is the launch system for Rutan's Tier One spacecraft and the DARPA X-37.

The Proteus is the current holder of a number of FAI world records for altitude (class: C1-e: landplanes 3,000–6,000 kg, Group: 3, turbojet), set in cooperation with NASA Dryden.

Scaled Composites, a wholly owned subsidiary of Northrop Grumman, actively markets the aircraft as a research platform, and has published a user's guide for planning proposed missions.

A small Airborne Real-Time Imaging System (ARTIS) camera, developed by HyperSpectral Sciences, Inc., under NASA's ERAST project, was demonstrated during the summer of 1999 when it took visual and near-infrared photos from Proteus while it was flying high over the Experimental Aircraft Association's AirVenture 99 Airshow at Oshkosh, Wisconsin.

[5] Then, in September and October 2000, during the Water-Vapor Intensive Operating Period, Proteus and NAST flew validation flights studying upper tropospheric water vapor and performing underflights of the Terra satellite.

The aircraft logged 126 flight hours, and was variously based out of Alaska, Hawaii and Japan, gathering data in coordination with ground, balloon and satellite sensor packages over the North Pole in March 2001.

Proteus was flown as a surrogate UAV controlled remotely from the ground, although safety pilots were aboard to handle takeoff and landing and any potential emergencies.

In April 2003, a second series of flight demonstrations focusing on "non-cooperative" aircraft (those without operating transponders), was conducted in restricted airspace near Mojave, California, again using the Proteus as a surrogate UAV.

Proteus was equipped with a small Amphitech OASys 35 GHz primary radar system to detect potential intruder aircraft on simulated collision courses.

[10][11] In July 2002, Proteus participated in Crystal-FACE, measuring tropical cirrus clouds, operating from Key West, Florida, flying as far south as Belize.

The mockup was a 23% scale model of a proposed four-person crew capsule (called the CXV) and its AirLaunch LLC-produced QuickReach II booster.

[needs update] On February 24, 2005, Proteus became Scaled's first bomber with the release of an inert 500-pound weapon over Nellis Air Force Base in Nevada.

[17] On April 27, 2006, Proteus flight tested a large pod designed to house a developmental version of the Multi-Platform Radar Technology Insertion Program, or MP-RTIP.