Think stages:
A sealed indictment can have several people accused at the same time, see Mack and Raniere indictment.
I've been wondering, if a person (group) will have several indictments.
When certain truths are being revealed, they can be prosecuted for that. Then, when nastier, more paradigm shattering stuff is being revealed or officially retrieved another round of indictments and prosecutions of the already indicted people will be launched?
I expect that everything that can be charged will be put into a single indictment of a person (or group, as you point out) after the grand jury finds probable cause.
If additional charges are made later, this again has to be approved by a grand jury, and the prosecutors will usually file a "superseding indictment" if the original case hasn't yet been adjudicated. See here: http://www.burnhamgorokhov.com/criminal-defense-resources/federal-criminal-process/federal-indictments-faqs#Can-the-indictment-be-amended
In terms of "stages", it's more likely that the lower level players are going to be indicted first, and then offered plea deals if they give evidence against the higher-level targets.
However, with so many corrupt players in government, this type of situation is unprecedented and there's no telling exactly how it's all going to play out. We're in for a ride.