I have high praise for Church and State for Mutants and Masterminds 1E. It provides a series of events that are likely to happpen, but leaves a lot of the bridging flexible, and accounts for different outcomes in earlier steps. It also has some good advice for how to deal with problem powers among the players and attempts to shortcut the mystery. The big drawback is that it will almost certainly require conversion, since it's two editions older than the current one, but the conversion process isn't too onerous and it comes with maps and artwork.
The twice I have played it, I have done so in 2nd Edition M&M. In both cases, the initial subway fight largely went well for the heroes, resulting in the Made Men turning tail and running without having to involve Mikhael or Rock 'N Roll for anything other than cleanup. The first time, the players tracked the Made Men through the tunnels and captured most of the remaining members (both Riot and Numbers made their escape earlier, having never revealed themselves as anything but citizens). In the second, only Arson got nicked, and the players seemed more interested in tracking down the source of his power armor than figuring out just why the Mafia had a group of supervillains attacking. In both cases, the players were more interested in Mikhael than in Rock 'N Roll and both times, they decided early on that he must be the villain of the adventure, spending a great deal of time trying to make him "slip up" and reveal his evil plans.
Feeling that there needed to be some downtime in between capturing the Made Men and the trial, I gave the players some other potential hooks and they largely dropped the investigative aspects, assuming that the Made Men were just hired guns. The first group wasn't really interested in the trial scene, so I played it offstage, with the Made Men being put away, but without a death penalty scene of any sort. With the second group, I'll admit that I muffed the trial scene, having not prepared properly, so after a few desultory rolls, I simply gave the verdict, namely that only Arson got convicted. The players had a good time trying to track down clues for the murder mystery, although they failed to catch the actual culprit, only catching the person behind her.
As I mentioned before, neither group of players trusted Mikhael, and the rather extensive set of example NPCs was useful in that I always had another name to pull out when they did more snooping at the church, although I also feel like it led them down the wrong path in some ways. After all, why would I take the time to flesh out NPCs unless this were the main villain? :-P Metagaming at its finest. When it came to the death of Father Candella, they did minimal investigating and largely attempted Diplomacy checks with Mikhael to try to convince him to let the police handle things. Well, largely diplomacy... one of the players played an ultra-conservative Captain America kind of guy and his bias against Rock's communist leanings led to him making a long declamatory speech about the evils of "his sort" which I suspect wasn't entirely just a character-based speech (I probably should have taken a cue from when he was GMing a segment of the game and cast the Occupy Wall Street people as evil terrorists out to destabilize the glorious empire of the United States). Ultimately, they wound up getting both sides to stand down, but only barely, and largely under a detente of "wait until we see what the evidence shows". Unfortunately, that group fell apart, so I never got to get them to the point where I could have the grand confrontation between the two sides. The second group eventually accepted that Mikhael was not behind the current crisis, although they still keep suspecting him of something nefarious, to the point where it's almost a running joke that when something bad happens, they assume Michael must be behind it.
So, final summation of my experience is that the module offers a lot of flexibility for when things happen and provides opportunities to do roleplaying and non-combat skill checks to investigate the situation. The maps are well laid-out and there's just enough info on miscellaneous NPCs to keep your players feeling like there's more depth to it. Pretty much any scene is skippable (and in fact, several only happen if the PCs make certain decisions or fail at prior scenes) and a lot of them can be switched around, and it's easy to interleave other adventures as long as you're not worried that your players will get confused as to what is from where (although it can be amusing to make them realize that not everything is connected). Minus side of the modularity is that you might wind up skipping whole sections because the PCs decide that they have better things to do or because they take different courses of actions. This is a module that's pretty good to run over and over again.