Use fairs and f tilt to cancel her missiles, or just shield or jump. Stay below her since thr worst samus can do without disjoints ar3 nair and dair. Missiles aren't too much of a problem. Just don't give samus space. Always apply constant pressure. Samus is slow enough in the air that you can catch her relatively easily. Don't be above samus too often... hmmm. What else do I know...
If they use fire, watch your spacing. If they fight like me, up smash will be a problem. And f smash if you misspace or are read
I don't think fire mode can combo well out of throws.
Ice mode can. If your fri3nd is good at following up on throws, ice mode will hurt. Samus can only combo out of down throw, and this is di dependent. If you di in, you get up smashed of naired. No di and the same thing. Di out and you get faired. Or at high enough percents, di out and get off scot free. Youll never make that high if your fri3nd is good though.
Fire power missiles are more dangerous in this matchup so watch out for those. Followed by ice homing, ice power, and then fire homing. Hom7ng missiles can get cut out of the air with your sword. Power missiles are harder to time a hit on, but maybe you should just guard or jump.
Tipped up air is your friend.