If it was discussed before just ignore it....
There are several possibilities:
- Rouvelier - he is obviously after Allen and Cross will be one the way should he wish to take 14th out. Better to take care of problems fast then wait for them to become bigger then they already are. Problem is that he did into act through Link and is dening it himself (not surprising though ;P), and well, get the feeling that it really is not him.
- Pope and Co - for the same reasons.... or for some additional ones. We know nothing about their goals except for exterminating Noah, which may not be the only thing they care about. Not ot mention the possibility of Noah infiltrating the very top if church and giving commands from there.
- Noah themselves - for obvious reasons... I don't really see it that possible, considering they had most likely established the new system of base protection (if it is not there why move the base at all) thats suppose to block infiltration unless its Allen who moves teh gate.
Maybe there are some others which i did not think of.... But well, this three are main suspects.
As for is Cross dead or not... The innocence becoming incompatible is a good argument for it, but I can't really belive in it that easily after all those revivals of main characters who were suppsoed to be dead before. So i'm still not sure.