>>86157375He was convinced that Frank was fucking losing it, so he stuck him in an underground prison to cool off, and in the hope that he could bring him back from the brink by forcing him to confront his repressed humanity (the prison was decked out like Frank's old house, complete with things like old photos and home movies that Micro got from Maria's family).
Anyway, while Frank alternated between freaking out and stewing, Micro started training a new Punisher (
http://www.marvunapp.com/Appendix/cruzcarl.htm) who would cover for him while he was locked away.
When Frank escaped, he was pissed and went after Micro. The two fought, and it's left ambiguous as to whether not Frank (who inevitably won) would have killed him since the building they were in was blown up by a psycho S.H.I.E.L.D. agent, killing Micro while Frank was seemingly struggling to pull the trigger on him.