The ship seen following Samus' ship at the 100% ending of Metroid prime 3: Corruption is widely believed to be the ship of the hunter Sylux from metroid prime hunters. It would fit the time line seeing as the order of metroid's story is:
Metroid/Metroid prime/Metroid prime hunters/metroid prime 2/Metroid prime 3/Metroid II: the return of samus/Super metroid/Metroid other M/metroid fusion.
Seeing as hunters is before the mysterious ship at the end of corruption, it could fit. It could also be Sylux because A) he/she wants samus dead which would explain why he/she would be following samus and B) because the ship in the end of corruption is almost identical to the ship seen in hunter's.