A translation of Namco x Capcom's script has surfaced and with it comes plot details of the Rockman DASH portion of the game.
Taking place in between DASH 1 and 2, Juno is inexplicably revived to reap vengeance upon "the Decoys" (humans). Although considered non canon (due to several inconstant plot details), the story sheds some light on the functions of Eden (Carbon Reinitialization Satellite) as well further insight to the world of the series.
Without further adieu, here is the translated DASH plot as summarized by "Zan:"
"He (Juno) introduces himself without any memory of the DASH1 events. Roll wonders who it is. Tron and Rock however are immediately alarmed by his presence as he is the one Rock fought inside of the Main Gate. It seems that as a result of the DASH1 events, Juno's previous body was destroyed by Rock and his memory was almost completely erased by Data. His current self is a new Rockman Juno with only portions of his memory restored because the reconstructive process did not entirely succeed. (The reconstruction was carried over by crossover character Grand Master Meio who became interested in the technology used to create Juno. He also seems to be responsible for Juno's new body.)
Rock knows he has to destroy Juno before he regains his memory, as Juno would attempt to wipe out the Decoys again. Over time, Juno begins to realize he met and fought Rock before, Rock's strong emotional responses toward Juno also motivate him to regain his lost memory. As Juno's memory recovers, Roll too is informed about the mysteries of Rock's past. The name Rockman Trigger is brought up and Juno notes that it is significant, he also begins to speak to Rock as his superior "Lord Rockman Trigger." (Rockman Trigger-sama?)
Juno plans to reinitialize the Decoys of Earth using Eden and by the magic of crossover he's conducting an experiment to enhance Eden's area of effect beyond regional scope, able to terminate all Decoys on the planet. Juno however is constantly met with resistance and begins showing irregular behavior, his logic systems seem defected as he starts blaming others for own failure. Rock questions him about it not even aware of the meaning of the term, despite realizing this is what is happening to Juno. Having turned completely irregular according to Rock, Juno completes his experiment and gives us previously unknown information about the nature of Eden.
The final battle between Juno and Rock finally occurs, Juno regains his memories and realizes Rock's memory isn't complete either. Roll's interested in knowing what this "Trigger thing" is. And Juno explains Rock is Rockman Trigger Purging Officer First Class. Roll questions who Rock is and Rock has to reassure her he is himself, his name is Rock Volnutt. Rock defeats Juno and says his final farewell to him."