▁the ▁real ▁C IA , ▁she ▁disco vers ▁that ▁her ▁father ▁has ▁long ▁been ▁in ▁the ▁same ▁position ▁and ▁they ▁learn ▁to ▁work ▁together ▁to ▁bring ▁down ▁SD - 6 . ▁Jack ▁often ▁used ▁his ▁position ▁as ▁Slo ane ' s ▁chief ▁of ▁operations ▁to ▁structure ▁miss ions ▁to ▁the ▁C IA ' s ▁advantage . ▁When ▁Ir ina ▁D ere v ko ▁makes ▁her ▁re app earance ▁in ▁Season ▁ 2 , ▁Jack ▁must ▁also ▁deal ▁with ▁his ▁un resol ved ▁feelings ▁of ▁love ▁and ▁bit tern ess ▁towards ▁her ▁while ▁continu ing ▁to ▁perform ▁his ▁job ▁at ▁SD - 6 ▁and ▁the ▁C IA . ▁With ▁SD - 6 ' s ▁destruction , ▁Jack ▁found ▁himself ▁finally ▁able ▁to ▁grow ▁closer ▁to ▁his ▁daughter . ▁ ▁Sydney ▁lear ns ▁in ▁season ▁ 2 ▁that ▁Jack ▁subject ed ▁her ▁to ▁Project ▁Christmas , ▁a ▁project ▁that ▁trained ▁and ▁hard w ired ▁potential ▁sp ies . ▁Sydney ▁initially ▁believed ▁that ▁this ▁programming ▁had ▁taken ▁away ▁her ▁choices ▁in ▁life , ▁but ▁in ▁Season ▁ 3 ▁disco vers ▁that ▁it ▁had , ▁in ▁fact , ▁protected ▁her ▁aut onomy ▁and ▁made ▁her ▁imm une ▁to ▁brain w ash ing ▁by ▁the ▁C oven ant . ▁During ▁Sydney ' s ▁two ▁year ▁disapp earance ▁between ▁Se asons ▁ 2 ▁and ▁ 3 , ▁Jack ▁was ▁again ▁taken ▁into ▁cust ody , ▁held ▁in ▁solit ary ▁conf in ement ▁for ▁a ▁year ▁because ▁of ▁his ▁working ▁with ▁uns an ction ed ▁sources ▁( including ▁Ir ina