A possible idea for a 'Soul Eater Soul Gets Sick' fanfiction is that Soul's sickness is related to the amount of souls he has consumed. Maybe he's absorbed some corrupted souls by accident, and now they are causing an internal conflict within his own soul. This could lead to symptoms like weakness, strange hallucinations, and an inability to fully transform into his weapon form. Maka would then have to figure out a way to either expel these corrupted souls or find a way to purify them within Soul.
One idea could be that Soul's sickness is caused by an unbalanced resonance with Maka. Maybe they've been overusing their Soul Resonance in battles and it's taking a toll on Soul. Another idea is that an enemy has cursed Soul, making him sick in a way that weakens his combat abilities and his connection to his weapon form. For example, the curse could make it painful for him to transform.
Well, perhaps Soul gets sick because he's been exposed to some sort of dark magic that's seeping into his very essence. In the fanfiction, this could lead to Maka having to find a way to purify his soul without the use of their normal combat techniques. She might have to journey to a special place or seek out a particular character who has the knowledge to heal Soul. It could also be that Soul's sickness is a manifestation of his inner turmoil, like his doubts about his role as a weapon and his relationship with Maka.