(This is my first calc)
So, i believe that you already know that Samus´ speed is pretty high. But how high is it actually?
To answer that question, i´ll take a look at Metroid Prime Hunters: According to the Metroid wiki, the entire franchise takes place in the milky way galaxy, with the exception of Prime Hunters, which takes place in a galaxy called "Tetra". That means that Samus´ ship is sufficiently fast to perform intergalactic travel in short timespans. Ridley is shown to be able to outpace said ship , with Samus being able to tag his speed . Since there is no known value for the distance between Tetra and the milky way, i´ll just use several galaxies´ distances to the Milky Way, namely those of the CMa Overdensity (the galaxy closest to the Milky Way), Andromeda (the closest galaxy that is comparable in size to the Milky Way) and UDFy-38135539 (the galaxy furthest from the MW) to calculate the feat. Chronologically, the events of MPH are said to happen in the timespan between the first two Metroid Prime games, which, according to SomebodyData, ranges from 1 to 11 months .
So, let´s do some math now!
The distance between the CMa Overdensity and the Milky Way is 42.000 light- years (less than half the MW´s diameter) and was covered twice, which means that the low- end for Samus´ speed is:
84,000ly/(11/12)y=91,636.36... c
84,000ly/(1/2)y=168,000 c
84,000ly/(1/12)y=1,008,000 c
Wow, that´s quite a bit, isn´t it?
Andromeda is 2.5 million light- years away from the MW. Again, that distance was covered twice, so the mid- end is:
500.000.000ly/(11/12)y=5,454,545.45... c
5.000.000ly/(1/2)y=10,000,000 c
5.000.000ly/(1/12)y=60,000,000 c
Okay, that´s quite large already. But the high end is even more ridiculous. UDF-38135539 is 30.3 billion light- years away from the MW, which leads to a high end of:
60.600.000.000ly/(11/12)y=66,109,090,909.09... c
60.600.000.000ly/(1/2)y=121,200,000,000
60.600.000.000ly/(1/12)y=727,200,000,000
Thus, we have a low end of 91,636.36... c, a mid end of 10,000,000 c and a high end of 727,200,000,000 c.