The gunships in Metroid II, Super Metroid, and Metroid Prime 2 all bear extremely close resemblance, so they are all also probably the same ship with minor upgrades each time.
The ship from Metroid Fusion is a completely different ship from any of the other games. When Samus becomes unconscious as an effect of being infected by an X Parasite, her ship (believed to be the same one from superMetroid metroid2, metroidSuper 2,Metroid and metroidMetroid primePrime 2: echoes, as it bears very close resemblance to each of them, and, considering the chronological order in which metroid fusion takes place, this would make sense) drifts into an asteroid field. The ship's emergency systems eject Samus in an escape pod a few seconds before the ship collides with an asteroid, causing it to explode. The Federation gives her the purple ship featured in Metroid Fusion after her surgery as a replacement. This may suggest that Samus actually has insurance for it, which would be slightly comical. The new ship is also linked to Adam, Samus's compuerized CO.
