Most recall law provide for a resignation period (in this case 10 days) for the official to resign to ward off the recall. What happens if they resign after that period? While I think the chance of this happening for Walker is beyond remote, in general this is not just an academic question -- we saw a similar instance in a Colorado school board case this year.
According to this reporter at the Capitol Times (who uses the John Doe investigation as a jumping off point:
If Walker resigned within 10 days of the recall petitions being certified by the GAB, he would not be on the ballot and other Republicans would be able to vie for the nomination in a primary. Meanwhile, Lt. Gov. Rebecca Kleefisch would become governor and could appoint a new lieutenant governor. Nothing, however, would stop the recall election from going forward.
The winner of the gubernatorial election would assume the office.
However, if Walker were to resign more than 10 days after the recall petitions are certified, his name would still appear on the ballot. Assuming voters would not favor an indicted, resigned governor, Republicans would likely be forced to mount some type of write-in campaign to try to prevent the Democratic nominee from being elected.