There have been plenty of baseball scandals in recent history and most of them have surrounded the use of Performance Enhancement Drugs. In 2007 a report was published informally called "The Mitchell Report" that investigated on the use of illegal substances in MLB.
Jose Canseco released his book Juiced where he admitted to using PEDs and name dropped plenty of other players such as Mark McGwire, Rafael Palmeiro, Jason Giambi etc. as fellow steroid users.
A nutrition center BALCO was accused by federal authorities to supply steroids to top players like Barry Bonds and Jason Giambi. A congressional hearing was setup as part of the investigation.
Baseball Commissioner Bud Selig appointed former senator George J. Mitchell to lead an investigation after a book Game of Shadows was released, chronicling Barry Bonds' steroid use.
Selig didn't explicitly announce Bonds as the motive of investigation. HIs aim was to investigate past and then-present high profile players on the alleged use of PEDs.
Mitchell investigated into the matter with the MLB Players' Association non willing to cooperate. Mitchell got hold of three people, Kirk Radomski, Brian McNamee and Larry Starr for having supplied PEDs to many players for ages.
The report focused on the ill effects of PED use and how it affected the minds of the young people watching their favourite players use them. It also listed down 89 players who were confirmed of having used PEDs and steroids.
Immediately following the findings of the report were released, Bud Selig held a press conference declaring stricter action against drug use and stating that some players on the list might receive disciplinary action.
MLB has stricter rules now when it comes to usage of drugs. Even after the Mitchell report other scandals such as the Barry Bonds' perjury case and the Biogenesis scandal followed.
For the last 10 years the MLB is free of any major scandal. All fans would be hoping it stays that way.