The injury to Joe is legitimate and not a part of the storylines. No word yet on when he will be back in action but he's suffering from a right foot injury and will be undergoing an MRI. As noted, Joe announced on RAW that he will be in the 30-man Royal Rumble match later this month.
"During his match, [Samoa Joe] felt a pop at the bottom of his [right] foot," said WWE Senior Ringside Physician Dr. Chris Amann. "We took a look and believe he has a plantar fascia rupture, which is a thick tissue rupture under the foot. We will get an MRI to confirm. Treatment includes a period of immobilization in a boot with crutches and platelet rich plasma injections."