Some of us may have had our doubts about Scott Thompson’s claim that he had nothing to do with the perpetuated myth about him having a computer science degree, but regardless he has agreed to step down from his position as CEO at Yahoo. As we reported earlier he will be replaced by Ross Levinsohn who was previously heading up Yahoo’s global media division.

Thompson’s resignation along with some new appointments to the Yahoo board marks a victory for activist investor Dan Loeb and his investment firm Third Point, but as the Wall Street Journal reports, it may be the beginning of a new battle for ex-CEO Thompson.

According to the 54-year-old Thompson, he has very recently been diagnosed with thyroid cancer and has already begun the treatment process to help fight the disease. Over the weekend he shared brief details with members of the Yahoo board and cited them as the primary cause for giving his resignation. He also said there would be no public announcement since he wanted to keep the details of his disease private.

If you remember back to early last week, Yahoo announced a formal investigation into Thompson’s false credentials. Recently Third Point put huge stress on the Yahoo’s board to take action against Thompson and other Yahoos who allegedly provided false credentials and seemingly deceived their way into positions at the firm.

Thompson’s resignation is the second we’ve seen over the controversial false credentials and heated proxy battle with Third Point. Patti Hart, who played an instrumental role in Scott Thompson being hire at the firm, resigned last week. As of this mourning, several of Yahoo’s board have also agreed to step down in order to make room for Third Point’s main man Dan Loeb, leader of the proxy battle, and his colleagues.

According to inside sources at Yahoo, Thompson is leaving with a sizable severance package, and presumably, his reputation still intact. No word on if the investigation of his credentials is still going forward with the private law firm Yahoo hired, but it looks like the proxy battle with Third Point has finally come to a head and Third Point is the big winner.