The Australian has been out for six weeks after sustaining ankle fractures during qualifying at Indianapolis - although Brno was the first race he missed as he braved the pain to finish fourth on the US circuit.
Despite therefore missing the last three rounds, Stoner could still play a vital role in the championship.
Honda team-mate Dani Pedrosa can still seal the 2012 crown, but only if he wins the remaining four events and current points leader Jorge Lorenzo finishes third or lower.
Stoner says he will find out what level he can ride in the first practice of this weekend's Japanese Grand Prix.
"The first session on Friday will be crucial to see how my ankle feels in the boot and the degree of movement I have and pressure I can apply," he explained.
"The Motegi circuit is very stop-start with a lot of hard braking and accelerating, it's pretty tough on the body and physically quite demanding."
Stoner said he was excited to be returning, adding: "It's going to be great to see all my team and get back on my bike in Motegi this weekend.
"The last six weeks have been pretty tough for me, I've had to sit around and rest my ankle, get some physio and try to occupy my time - thankfully I've had [daughter] Ally around to keep me occupied.
"I've been watching the races at home, I felt bad for Dani in Misano, but these things can happen - as they did for Jorge in Assen."
Pedrosa, who beat Lorenzo and Stoner to victory in last year's race at Motegi, said he was looking forward to the weekend.
"I love Motegi, it's a track with strong braking and strong acceleration," he said. "It's the most important weekend for Honda and I really enjoy the circuit.
"We have now the most demanding period of races ahead, but we will keep taking things step by step, thinking race by race.
"We had a good race there last year and we will work hard with the team to be as competitive as possible."
Lorenzo, Stoner and Pedrosa have all won just once at Motegi, in respective order over the last three years.
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