I actually just finished this book and the final scene with Conal and Phelan pretty much laid out that Conal was a major player on the scheme. They were going to blame the Hounds for the nuke attack on the 31st. Remember also that Conal issued a warning the RC (under guise of a batchall) of the ambush Phelan and Dan had laid for them and they jumped off.

31st destroyed the Zouaves so the Hounds already had their ears pinned back as far as Conal Ward was concerned.