In 2380 Romulan, Breen and Dominion Alliance is formed. The alliance is concluded and battle plans are drawn up for the invasion of the Federation and her allies, but long before this rumors were going long before the Enterprise was destroyed. The Federation then started to have problems, dissidents, some being placed to high in command with only one order, to stay put and wait, wait for the ORDER. Now, as time went, this Shadow group, associated themselves with the Romulans, the Breens, and finally the Dominians.
As to know who in command was part of the Shadow group, this never was totally figured out. Some names were found, evidence to corroborate those findings were logged and when we escaped we knew one truth. Some must have followed us, and a suspicion that the Brotherhood could be an offshoot of the Shadow group. The SFI are ever since working on the problem.