Whakakīhia te rerenga e whai ake nei: I te Hōngongoi 1999, i tohua a Jacoby hei kaiwhakahaere mō te mōhiohio (J2) i te Joint Staff. I tīmata tana tūranga ki te ārahi i ngā mahi matauranga ki te tirotiro i ngā mahi i te Balkan me Kosovo. I haere tonu ngā Operation Northern me Southern Watch ki te whakatinana i ngā rohe kore-rere me ngā herenga ki Iraq. Hei taapiri, ko te rererangi tirotiro a US Navy EP-3 i whakaekehia e nga Hainamana i te Moutere o Hainan whai muri i te tukinga me tetahi toa Hainamana i nga mahi i runga i te Moana o Haina ki te Tonga me te whakaeke ki
I tū te USS "Cole" ki Aden, Yemen. Ko tenei kaupapa whakamutunga i akiaki i te rereketanga nui o te huarahi ki te wetewete i te riri riri me te tautoko ki nga ope whakahaere i whakauruhia ki te Joint Intelligence Task Force, Combating Terrorism (JITF-CT) e mahi ana i raro i te aratohu a te Joint Staff J-2 hei waahanga o te Defense Intelligence Agency. I tohe a Jacoby mo te whakapiki i te tahua mo te JITF-CT i te ahiahi o te Mahuru 10, 2001 me nga kaimahi matua o te Komiti Whiriwhiri Tuturu o te Whare mo te Maatauranga. I roto ia i te Pentagon i te wā i whakaekehia ai i te 11 o Mahuru, 2001. I arahina e ia te tu-ake o te JITF-CT, i kaha ki te whakamahere matauranga mo te Pakanga Ao ki te Whakamataku me nga mahi hoia i Afghanistan, i tirotiro i nga mahi a J-2 i te waahanga tuatahi o nga mahi whawhai i Afghanistan, a he mea nui ki te whakawhanake me te whakatairanga i tetahi kaupapa whakahaere e kiia ana ko "2 Plus 7" i noho hei pokapū mo nga mahi a te US ki te whakakore i te whakahaere Al-Qaeda me te whakaeke i tana tari whakahaere me te whakamahere. I arotahi te kaha ki nga mahi ki nga kaiarahi e rua me nga kaiwhakahaere whakahaere e whitu. Ko te hua he whakahekenga nui i roto i nga kaha o te whakahaere. I whakaotihia e Jacoby tana whakawhitinga kotahi tau hei Joint Staff J-2 i te Hurae 2002.