Nyorai kupfuurira kweiyi ndima - Muna July 1999, Jacoby akagoverwa somutungamiriri wezvemashoko (J2) paJoint Staff. Kutonga kwake kwakatanga nokutungamirira nhamburiko dzokuongorora mabasa muBalkan neKosovo. MaOperations Northern neSouthern Watch akapfuurira kuita kuti nzvimbo dzisina kubhururuka dzipfuurire uye zvirango zvinopesana neIraq. Mukuwedzera, ndege yeU.S. Navy yeEP-3 yakabatwa neChina paHainan Island zvichitevera kurwisana neChina yehondo panguva yekuita pamusoro peSouth China Sea uye kurwisa USS "Cole"
kwakaitika muAden, Yemen. Chiitiko chekupedzisira ichi chakakurudzira shanduko yakakosha pakuongorora kwehugandanga uye kutsigira masimba anoshanda ayo akaiswa muchirongwa cheJoint Intelligence Task Force, Kurwisa Ugandanga (JITF-CT) inoshanda pasi pekutungamirirwa kweJoint Staff J-2 sechikamu cheDefense Intelligence Agency. Jacoby akanga achitsigira kuwedzerwa kwemari yeJITF-CT masikati aSeptember 10, 2001 nevashandi vakuru paImba yeParamende Yakasarudzwa Komiti yeUchenjeri. Akanga ari muPentagon pakarwiswa musi waSeptember 11, 2001. Akatungamira kumira kweJITF-CT, akashanda mukuronga kwehungwaru kweHondo Yenyika Dzese Kupokana nehugandanga uye mashandiro ehondo muAfghanistan, akatarisira zviitiko zveJ-2 panguva yekutanga kwechiitiko chekurwa muAfghanistan uye akabatsira mukugadzira nekusimudzira pfungwa yekushanda inonzi "2 Plus 7" iyo yakave nzvimbo yepakati yezviitiko zveUS kuputsa sangano reAl-Qaeda uye kurwisa hutungamiriri hwayo hwepakati uye mabasa ekuronga. Nhamburiko dzakanangidzirwa pamabasa mukurwisana navatungamiriri vaviri navakuru vanomwe vanoronga kushanda. Mugumisiro wacho wakanga uri kuderera kukuru mumano esangano. Jacoby akagumisa kuwedzerwa kwake kwegore rimwe seJoint Staff J-2 muna July 2002.