Kammala jumla mai zuwa: Alpha ya kasance mai aiki a lokacin Yaƙin Chechen na biyu wanda ya fara a 1999, da kuma na gaba
Tashin hankali a Arewacin Caucasus. A lokacin Yaƙin Komsomolskoye na 2000, an tura 'yan bindigar Alpha da ke da alaƙa da rukunin Yammacin Vladimir Shamanov na sojojin tarayya, a yunƙurin murkushe' yan bindigar Ruslan Gelayev a ƙauyen. A cewar tsoffin mayakan naúrar, ayyukan da Alpha ya halarta ya haifar da kama kwamandan Chechen Salman Raduyev a 2000, kisan kwamandan Chechen Arbi Barayev a 2001, kisan shugaban Chechen mai rabuwa Aslan Maskhadov a 2005, da kisan shugaban mayakan kasashen waje Abu Hafs a Dagestan a 2006. Bayan canja wurin alhakin ayyukan a Chechnya daga Ma'aikatar Tsaro zuwa FSB a watan Janairun 2001, kuma kafin manufar "Chechenization" da aka fara a 2003, membobin Alpha (tare da sauran ma'aikatan Rasha da 'yan kungiyar Chechen da ke goyon bayan Moscow) sun halarci aƙalla "ƙungiyoyi na musamman" guda 10 (, SSGs), waɗanda ƙungiyoyin kare haƙƙin ɗan adam da masu sa ido na waje suka ɗauka a matsayin ƙungiyoyin mutuwa. An yi imanin cewa SSGs sun kasance a baya da yawa daga cikin "sunan / adireshin tsabtace" ("imeny/adressny zachistki"): yawanci hare-haren dare da maza masu rufe fuska a cikin motocin da ba a san su ba, da nufin takamaiman mayakan 'yan tawaye na yanzu ko na baya, magoya bayansu, danginsu, ko wasu fararen hula don ko dai bacewar tilas ko kashewa ba tare da shari'a ba. A shekara ta 2005, kungiyar kare hakkin dan adam ta Human Rights Watch ta bayyana cewa bacewar mutane ya kai matsayin aikata laifuka ga bil'adama, kuma cewa "Rasha tana da bambancin rashin daraja na kasancewa jagora a duniya a cikin bacewar tilas". UFSB na Chechnya kuma ya kafa wani rukunin Alpha na gida, wanda aka yi imanin yana da kama da rawar da SSGs ke takawa.