MLB allowed a plea bargain in the first of the Biogenesis cases. (see article on this blog for June 16, 2013) This was the result of two meetings between Braun and MLB. At these meetings, Braun did not offer testimony, he was simply presented with MLB’s evidence. He agreed to a 65 game, or rest-of-the-season suspension.
As described earlier here, the evidence was non-analytical positive evidence much like the evidence used in USADA’s case against Lance Armstrong.
This evidence is other than drug test evidence but is equally effective in determining use, hence, a violation of the MLB drug use rules.
The most curious part of this is that even with the evidence, MLB chose to bargain for what it could get and did not simply suspend Braun to the limits of the rule,  possibly 100 games.
The reason for this is that MLB has had a difficult time with arbitrators in such cases. The most notable is the Steve Howe case where an arbitrator denied efforts to suspend for life a player whose drug use was epidemic on the basis of a failure to provide counseling instead. Last year, Braun was accused of positive drug test violations and the arbitrator dismissed the case based on a chain of custody error.
To avoid such an outcome again, MLB is bargaining over suspensions. Braun will lose $3.25 million in salary this year, but retains the more than $100,000,000 left on his contract with the Milwaukee Brewers. The question I want answered is whether the Brewers are planning to attack his contract itself, claiming breach on the theory his drug use was a violation of that contract.
The plea bargain process is underway with the approximately two dozen other players named in Biogenesis. Foremost among these is Yankee player Alex Rodriguez. Here the topic is a possible lifetime ban, but the player will negotiate something much shorter, unless MLB decides to suspend and go to arbitration in this case. At some point it has to do this.
The Yankees have the right to challenge the Rodriguez  contract as well and it is through breach of contract actions that MLB and its teams will realize real clout in the drug use cases.