Mega Man is neither apprehended nor slain. HOPE!
I'm assuming you've all seen the new trailer for Phoenix Wright and Nova for Ultimate Marvel vs. Capcom 3. Along with the gameplay reveal of the new characters, some of the released gameplay videos also showed off some new stages. There's a certain detail in one of those stages that is causing a lot of buzz.
In the stage 'Future Past' there is a wanted poster showing off a bunch of characters with either the label 'slain' or 'apprehended'. Much like the Uncanny X-Men comic cover which features mutants from the X-Men series, this poster shows off a lot of characters from Marvel vs. Capcom 2. Each character already has a mark. Everyone except one character that is.
List of Apprehended Characters – Colossus Ruby Heart Gambit Hayato Psylocke BB Hood Unknown?
List of Slain Characters – Cyclops Marrow Ice Man Jin Saotome Cable Amingo Captain Commando Son Son
Characters with no label or an obscured label - Mega Man
Missing Characters – Thanos Blackheart Venom Juggernaut Omega Red Rogue Sabretooth Silver Samurai Spiral Anakaris Roll Servebot Cammy Charlie Dan Dhalsim Guile Ken Bison Sakura Zangief Uncanny X-Men #141