What could it be?[]
There are many theories into what the spacecraft could be. Many people have noted that it bears a slight resemblance to Sylux's Delano-7. However, its Phazon-blue colouration has led an equal amount of people to believe that it belongs to the supposedly deceased Dark Samus. Here are a few theories on the origins of the ship.
•Sylux might have met Dark Samus at some point during his life and managed to steal her ship in some form or another.
•Another states that Dark Samus may have abandoned her ship at some point during her life (finding out she no longer requires a ship for space travel) and left it. Sylux then found it and abandoned the Delano 7 and took her ship (thinking its far more superior to his)
•Another more likely theory states that Dark Samus stole the Delano 7 from Sylux and killed him in the process. She then made extreme modifications to the ship.
•It is also possible that this ship's resemblance to Sylux's Delano-7 is because both were designed by the Galactic Federation, which would imply that the unique ship in question is also a prototype, possibly a second version of the stolen Delano-7. Considering that an entire fleet of Federation ships was present during the final siege of Phaaze, it is probable that this ship was among them, and Dark Samus somehow took control of it in order to escape the destruction of Phaaze. This is perhaps the most likely explanation, as Sylux's appearance in the 100% ending of MP3 would be a non sequitur.