Jolly Roger Affair
The Jolly Roger Affair (also occasionally called the Jolly Roger Plan) was a clandestine ComStar operation starting in 3001 that sought to increase the fighting between the Draconis Combine and the Lyran Commonwealth along their coreward (Periphery) border by sponsoring independent pirate forces.
Although a success in this respect, the operation went bad when some of the pirates turned against ComStar in 3004; Jolly Roger was subsequently terminated and covered up. It is not generally known to have occurred.
In 2997 the LCAF high command requested a slowdown in their offensive against the Draconis Combine to rest their exhausted troops. Although Archon Alessandro Steiner refused, the military found ways to deliberately delay and bog down their own offensive through bureaucracy. At the same time across the border, the DCMS had lost their fighting spirit under Hohiro Kurita's excessively centralized control and increasing paranoia; save for the (failed) attack on Hesperus II in early 3000 the Kurita military preferred to concentrate their efforts on the Federated Suns instead.
The Jolly Roger Plan
Always anxious to maintain the balance of power in the Inner Sphere in the ongoing Third Succession War, ComStar's First Circuit wanted to escalate the Kurita/Steiner fighting back to its previous levels. With only marginal endorsement of Primus Allen Rusenstein, the First Circuit ordered ROM in 3001 to enact a plan to supply pirate forces in the Periphery with combat equipment as well as financial and logistical aid to set up pirate operations in various isolated parts of the Periphery to stir up and escalate military conflict in the general area.  
ComStar covertly provided renegade MechWarriors with BattleMechs, Fighters and DropShips and even went so far as to provide them with bases on lost Periphery worlds that had been rediscovered by the Explorer Corps years earlier; the existence of these worlds had been kept secret from the Successor States. No trace could ever be found linking any of the equipment, financial aid or information to ComStar. 
The plan went quite well initially. The pirates accepted the aid and equipment without asking too many questions about its origin or the intentions of their benefactors. Several new Bandit Kingdoms sprung up in short order. By spring of 3002 the Lyran Commonwealth repeatedly came under attack from Periphery bandits, and within half a year the same pirates struck against the Draconis Combine as well. The Commonwealth and Combine accused each other of having sponsored the pirate attacks and tensions flared up. Suspicious about each others motives and pressured by the raids, both governments moved entire regiments of key troops out to their Periphery borders. 
Within ComStar, this was seen as a great success at covertly exercising power in the Periphery and manipulating the Successor States. In the light of the apparent success, Primus Rusenstein did not hesitate to accept the credit. 
Backlash and Termination
In 3004 two of the Jolly Roger Bandit Kings, "Black" Jack McGirk and Darleen Dunson, became lovers and joined forces. Between them, they fielded almost a regiment of BattleMechs and support forces, constituting an unusually strong force by Periphery standards which they used to conduct a series of lightning-fast raids along the Commonwealth/Periphery border. Following their example, other pirates also joined forces to gear up on choice targets. 
Jolly Roger quickly spun out of control. On orders of the Primus, Precentor Kintero of the ComStar Guards and Militia tried to negotiate with the renegades to bring them back into line with ComStar's agenda. For reasons unknown the talks escalated to the point that Kintero's party had to fight their way out of the bandit's holdings. Darleen Dunson was killed in the process, and ComStar thereby earned the wrath of "Black" Jack McGirk who felt his former benefactors had betrayed him and was infuriated over the death of his lover. He laid waste to the HPG compounds on the worlds of Lost and Canal, killing dozens of personnel in the rampage. 
While the Lyran suspicions were allayed with a cover story claiming that the HPGs had only suffered light damage from Periphery raiders, Primus Rusenstein ordered the First Division of the ComStar Guards and Militia to exterminate the renegade pirates. This was achieved, but it cost ComStar dearly: McGirk's forces achieved a 2.3 to 1 kill ratio against the inexperienced ComStar Guards in a three-day battle on the isolated, unmapped world of Trisha, some eight jumps into the Periphery, before being wiped out. 
Although he really had little personal responsibility for the affair, the failure was laid at the feet of Primus Rusenstein rather than on the actual sponsors of the plan, and severely damaged his position and authority. The Jolly Roger Affair, together with the unexpected appearance of the five regiments of pristine 'Mechs of Wolf's Dragoons seemingly out of nowhere, led to his forced resignation from office a year later.
- ComStar, p. 49 "The Jolly Roger Affair"
- Field Manual: ComStar, p. 13 "The Com Guards - Bait and Switch"