As per official news today Captain Laurena Bowells recovered escape pod with unconscious Lt. Commander Shepard. There are still a few facts unknown to public. Lt. Commander Shepard was found aboard escape pod from Sovereign Class vessel with valid Federation transponder signal. She was heavy injured and unconscious, in addition there were traces of drugs found in her blood system. After Lt. Commander Shepard woke up she admited to not remembering large part of time spent aboard vessel that holded her, possibly side effect of one of the drugs she was injected with.
With curent information we cannot exclude possibility of a security breach, nor possibility that Shepard could cross sides under extreme duress. Currently all evidence and intel point to the operation of a Federation starship at same time and same area as kidnapping took place. It is highly unlikely that Federation as a whole was directly involved in the kidnapping. However, it is possible that some factions within the organization were directly involved, since they were delivering hardware and likely intel crucial to succed in capturing small vessel like Aerowing in open space. In addition, the flight recorder was missing from the craft. While that doesn’t prove that the Federation took part in the incident, it is still important information. There was clearly some intent to hide whatever was recorded by sensors by unknown parties.
Any information related to status of Lt. Cdr. Shepard is to be classified and not to be discussed unless proper authorization is obtained and security procedures followed.