When Scott Thompson decided to leave his post as President of PayPal to join Yahoo as CEO, it reportedly came as a shock to eBay CEO John Donahoe.

And it was a surprising move according to some industry observers.

After all, Thompson was ditching Ebay’s fastest growing division to join a company that has been in decline.

It’s a decision Thompson may regret for a long time.

Following the revelation that Thompson did not receive a computer science degree, as he had claimed on his resume, Yahoo found itself in the spotlight. One member of the Yahoo board of directors, who was on the search committee that hired Thompson, resigned, and angry shareholders were threatening to take legal action.

The situation came to a head yesterday when Thompson agreed to step down as CEO of Yahoo. According to one report, Yahoo will say that the resignation was part of a termination for “cause”, allowing Yahoo to part ways with Thompson without paying him severance and delivering some $6.5m in restricted stock units. According to another report, Thompson agreed to resign after learning that he has been diagnosed with cancer.

While there’s more to this story to be written, the big questions now are how interim CEO Ross Levinsohn will manage Yahoo’s affairs. Levinsohn, who has been at Yahoo since 2010, is best known for his role as President of Fox Interactive Media. Some to suggest that his background could lead him to pursue a more advertising-focused direction for Yahoo as opposed to the commerce-centric direction Thompson seemed to be taking.

There are also questions as to whether Levinsohn could seek to reverse Thompson’s aggressive patent strategy, which saw Yahoo sue Facebook in a lawsuit that has been a PR disaster for the once-great internet giant.

It will probably take a while for everything to play out. Levinsohn is Yahoo’s interim CEO, and while he’s obviously a viable candidate to take over the position permanently, don’t be surprised if Yahoo’s board of directors, which itself will be changing quite a bit, takes the appointment of Yahoo’s next CEO slowly, if for no reason other than to give the appearance that it’s being more careful about who it hires as the company’s chief.

In the meantime, one thing is for sure: Yahoo may have solved the problem of a CEO with a bad resume, but it still hasn’t solved the problems that Scott Thompson was hired to try to fix.