While the relationship between the communications organization ComStar and the newly formed Federated Commonwealth was cool but cordial in public, behind the scenes it bordered on open hostility. Under Primus Myndo Waterly the supposedly neutral Order became increasingly blatant in its efforts to manipulate and shatter the union of the Steiner-Davion realms, which had led to Davion suspecting the organization's neutrality was merely a façade and it actively opposed him. 
Things came to a head in fall of 3034 when MIIO agents deep in the Draconis Combine reported that the Combine had access to sensitive FedCom information that could only have been leaked by ComStar. In response, Prince Davion ordered Operation FLUSH, its goals to remove all ROM agents operating within the Federated Commonwealth and to expose ComStar's neutrality as a sham. 
Though a clandestine conflict, Operation FLUSH was a bloody and brutal war. In December of that year, MIIO staged snap sweeps which captured a number of key ROM agents among the large number of suspects. While the proportion of agents to innocent civilians taken in these sweeps was worrying, the method proved effective enough to see continued use. Newly invested Precentor ROM Anastasius Focht's response to FLUSH was to wage a war of confusion, ordering those ROM agents still operating in the Federated Commonwealth to plant false leaks and spread misinformation. While MIIO continued the search for ComStar agents, the misdirection led to an increasing volume of innocent high-ranking AFFC and FedCom government official incorrectly being targeted. 
Early in the conflict the Com Guards remained under ROM's operational command, with the increasing threat that Davion would order the targeting of the hated troops in his realm, Primus Waterly put the Readjustment Act of 3035 to the First Circuit. This reversed the situation and placed ROM under Com Guard control and created the position of Precentor Martial of ComStar to be filled by Anastasius Focht. While the Readjustment Act kept Davion from openly drawing the Com Guards in Flush, the creation of the Precentor Martial position also allowed Waterly to provide Focht with a role best suited to his skills, the Primus secretly disappointed with Focht's rather soft-handed response to Davion's offensive. Focht's replacement as Precentor ROM, Charles Seneca, was given much more direct orders to step up the conflict and to freely use assassination against FedCom agents who dared to attack the Order. For almost a decade, both sides proceeded to engage in a deadly game of cat and mouse and in all, 420 agents of both agencies had died when Davion finally ordered the operation to be wound down in 3044.
For both ComStar and the Federated Commonwealth the conflict ended at best in fruitless stalemate, but both claimed that they had gained the upper hand. Also, with both sides having directed increasing resources against the other, the agents of SAFE, Maskirovka and most notably the ISF had a easier time against both ComStar and the Federated Commonwealth. At its peak, over a quarter of the MIIO was devoted purely to Flush and this lack of resources prevented the organization from accurately gauging the strength of the DCMS prior to the War of 3039 and ultimately contributed to the AFFC's defeat.
- Historical: War of 3039, p. 66 "Shadow Wars - The ROM War"
- ComStar (sourcebook), pp. 61-62
- Intelligence Operations Handbook, p. 106
- Field Manual: ComStar, p. 13