I'm in the middle of a really long monster myself so I won't read all of it, but if you really can't tell, you can always just pick whichever department you have agents from, or you can do a co-authored mission. If you had a DIC Agent, you could team up with someone from DoGA and get rid of it together, and visa versa.

I praise you for taking on such a long fic, because ow, at least my 62-chapter thing didn't have really long individual chapters.