I'm pretty sure EXE has fought an Omnipresent being before, yeah? That's good for this fight then. EXE being 2 Universes is a problem yes, but Ness is Low 2-C with 2-C Passive Fate hax that scales to more Universes than EXE. That sounds like an issue, but EXE is no bad guy (though Ness and TOTU don't have knowledge on EXE, and the same applies to EXE). Though looking back at Supes vs EXE fight, apparently EXE starts with Matter Manipulation, Energy Manipulation, and Data Manipulation on a Low Multiversal Scale. This would obviously kill Ness but however, it isn't affecting TOTU (due to AP difference and Type 5 Immortality) in any way and therefore TOTU would be able to change Ness's fate (as he treats death and Incapacitation as a "bad dream") If The Player gets involved, then it can one shot EXE (though I'm pretty sure this requires Ness to use his Telepathy so idk about that argument. But if it happens, then good for Ness).
Typically, Ness opens up with a lot of status effect abilities ranging from Paralysis, Hypnosis (Sleep Manipulation), PK Flash (which is just really strong Light Manipulation that sometimes induce Confusion, Uncontrollably Crying, Paralysis, and at the Omega Level it's most likely an instant death), Poison Manipulation, and Sound Manipulation. Ness can use his shield, but I doubt it'll hold up against a 2-C.