Pondering this as a scenario for an AU fanfic:
Suppose that the Illusive Man's decision to send Shepard's squad into the Collectors' trap with the fake turian signal backfires and Shepard is killed trying to escape before the Collector ship's weapons come back online, but the other squadmates make it out alive and EDI still gets all the info on the Collectors being created from the Protheans, the IFF, etc.
I think that most of the alien crew members, and at least some of the human ones, are going to be furious with TIM and Cerberus at this point for getting Shepard killed. Miranda will insist that they carry on with the mission and try to assume command as Shepard's XO, at which point Jack, Tali, and Chakwas basically start packing their bags and demand to be let off the ship at their next stop.
Garrus, Mordin, Samara, and Thane aren't happy but aren't ready to walk off the mission just yet. Jacob is angry with TIM, seeing this as a violation of the "conditions" for his working with Cerberus, but also isn't sure he wants to call it quits yet. Zaeed doesn't really care as long as he's still getting paid. Kasumi doesn't make a decision right away but is starting to think this whole thing is riskier than what she signed up for. With the exception of Zaeed, some or all of this group may still need some persuading to stay with the mission somewhere before the end of the story.
While I do think Miranda would try to take charge in this scenario, I'm trying to decide whether she would still act as more of a Cerberus loyalist, happily showing the door to any malcontents and moving to have them replaced with established Cerberus personnel, or whether she would also be angry and distrustful of TIM at this point. I've long thought that sending the crew into a trap on purpose revealed a very paranoid, control-freak side to TIM's personality - you would think the Normandy crew could do a pretty good job of *pretending* to walk into a trap to get the data, and Miranda might see it as an implied insult to her abilities that TIM didn't tell her the truth. If she does start to turn away from TIM, I'm thinking that maybe she'll persuade everyone to stay by putting Jacob or Garrus in charge of combat tactics while she makes the broader decisions about which missions to pursue and when.
If I do this, the story will probably culminate with Miranda making the decision to destroy the Collector Base, but I'm not sure if she should be relatively firm in her Cerberus loyalties for a while at first or if concealing the Collectors' trap and getting Shepard killed would be enough for her to start questioning her affiliations.
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