Does Nova have some weird composite of her armors and equipment? I guess I'll assume so. I also don't have much knowledge on Master Chief, so I may be downplaying him.
Does Master Chief have any way of seeing through Nova's cloak or has otherwise dealt with invisible foes? If not, Nova is permanently invisible with the Tactical Stealth Suit, so she could just beat him up due to being physically stronger than him outside of direct impact, or she could drop a nuke from a safe distance away. Nova handles this Low-diff.
If he does have a way of seeing her, then Nova's still too durable for his lighter weapons to harm, and that would be the obvious choice for him to open up with against her. If he tries to fight her physically, she'll kind of easily overpower him. He'll have to rely on his heavy weapons, some of which barely scratch her and some of which would harm her bad, but she has lots of experience against the heavy weapons of the Tal'Darim. Meanwhile, she has various ways of hindering him, such as a holographic decoy that ca harm him and can be used to throw him off, flashbang grenades that are powerful enough to stun Marines through their polarized visors, has a forcefield of her own that's just as durable as she is, can teleport with the phase reactor suit (again, assuming its a composite since it isn't stated), and has various weapons to choose from in taking him down. Nova takes this with some more difficulty, but not that much.