Sonic and Knuckles, those are about the only two outta the games I’ve played or replace Knuckles with Tails or Shadow. Oh Ninian and Myrhh would do it too. Possibly other Fire Emblem charecters, but not likely.
Others would be any combo of Goku, Gohan, Spiderman, Gotenks, Vegeta, Superman, Doomsday, various X-Men, Dark Schneider(not sure about spelling), Hulk, Piccolo, Kuririn,Android 18, Android 16, any villian from DBZ and most from Superman, Akuma, Inyushua,Sesshomaru,Kiyko,other characters from Inyushua as strong as them(Magna versions). Yusuke, Hiei, Kurama, Kuwabara,Ani Toguro, Younger Toguro, Sensui, and pretty much anyone from stronger than Yusuke at the begging of the Dark Tournament.
Ryu,Godzilla,Vash,Knives,Mew,and Mewtwo(the movie versions). Most of these guys could do it by themselves, but characters such as Inyushua would need help.
If were talking strictly Halo and Metroid you’d have to stack the odds to beat them.
one combo that could kill anyone is god and budda. or how about some jedis or superman and Doomsday (the gut who killed Superman)
how about crishtorpher reeve and terri schiavo
(haha, i’m such a jackass)
Yea, ceartin Jedi could kill them. Yoda, Mace Windu, Obi-Wan, possibly Luke. Same with the Sith, Darth Vader(pre suit wouldn’t have much trouble), Darth Sidious, possibly Count Dooku. Samus would own the Jedi that were killed by the stormtroppers.
Wrath,Gluttony, Greed,Ling,Izumi,Hohenheim,Roy, and the Elric Brothers may also be strong enough as well. They all could probably beat Master Chief, but I don’t think they’d be able to take down Samus.
Spiderman would beat them both mostly due to the Spidey Senses.
I could go on and find more but that take way to long. They are plenty of VideoGame/movie/cartoon/ComicBook characters that are way outta Samus and Master Chief’s leauge.