A lot of people comment on Superman becoming a shill for the Government in this story, but to me it's explained pretty neatly: when he meets Batman in secret (also meeting Robin for the first time in a fantastic scene), they discuss how Clark's on the inside and Bruce is on the outside while working together despite their big staged battle of hostility. Clark helped the 'Mystery Men' from the inside and continues to do so. I remember a scene in which he is called by Faraday and isn't happy about it all and lets him know it, and I think it's a role he almost had to play. How could someone with his powers just fade away and not use them? He had to find a way, and he and Bruce cooked this up.