Improvements to the ship's defenses have been added since her launch.  One such improvement is a technology dubbed, "Sub-mode."  This technology, developed by the engineering crew of the USS Katana, originally combined the holographic emittors through the sensor array which would project an image around the ship giving her an appearance different from what she is.  This appearance, however, was easily over come by any scan of the image. When on a mission with the Katana, the technology was shared, and then improved upon improved by the, then. Chief Engineer of the Eagle, Lt. Tamara. Tamara routed the holoimage through the shield emittors.  The result is a more solid image, but shield capacity is reduced greatly.  The idea though, is to fool the enemy long enough to get in a first shot. Then the Sub-Mode can be turned off and full ship's defenses returned to normal. A further improvement to the sub mode was made when Ian Resork, the ship's CMO, and a shapeshifter, Left a part of himself in the neuro paks. This allows for a quicker and even more solid holo-image to be projected around the ship.

      Upon the successful return of the USS Voyager, The Eagle was recalled to the ship yards for experimental improvements. Added to the ship is ablative armor. The technology had been successfully incorporated in to the Voyager's systems and then added to the Eagle, The armor was added as an extra stability fator and must be engaged when the slip-stream engines are used.