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code/modules/awaymissions/capture_the_flag.dm

@@ -210,7 +210,7 @@
 /obj/machinery/capture_the_flag/attack_ghost(mob/user)
 	if(ctf_enabled == FALSE)
 		if(user.client && user.client.holder)
-			var/response = alert("Enable CTF?", "CTF", "Yes", "No")
+			var/response = tgui_alert(user, "Enable CTF?", "CTF", list("Yes", "No"))
 			if(response == "Yes")
 				toggle_all_ctf(user)
 			return

code/modules/awaymissions/corpse.dm

@@ -49,7 +49,7 @@
 		var/mob/dead/observer/O = user
 		if(!O.can_reenter_round() && !skip_reentry_check)
 			return FALSE
-	var/ghost_role = alert(latejoinercalling ? "Latejoin as [mob_name]? (This is a ghost role, and as such, it's very likely to be off-station.)" : "Become [mob_name]? (Warning, You can no longer be cloned!)",,"Yes","No")
+	var/ghost_role = tgui_alert(user, latejoinercalling ? "Latejoin as [mob_name]? (This is a ghost role, and as such, it's very likely to be off-station.)" : "Become [mob_name]? (Warning, You can no longer be cloned!)",,list("Yes","No"))
 	if(ghost_role == "No" || !loc)
 		return
 	if(QDELETED(src) || QDELETED(user))
@@ -595,7 +595,7 @@
 	job_description = "Space Bar Patron"
 
 /obj/effect/mob_spawn/human/alive/space_bar_patron/on_attack_hand(mob/user, act_intent = user.a_intent, unarmed_attack_flags)
-	var/despawn = alert("Return to cryosleep? (Warning, Your mob will be deleted!)",,"Yes","No")
+	var/despawn = tgui_alert(user, "Return to cryosleep? (Warning, Your mob will be deleted!)",,list("Yes","No"))
 	if(despawn == "No" || !loc || !Adjacent(user))
 		return
 	user.visible_message("<span class='notice'>[user.name] climbs back into cryosleep...</span>")

code/modules/awaymissions/signpost.dm

@@ -16,7 +16,7 @@
 	. = ..()
 	if(.)
 		return
-	if(alert(question,name,"Yes","No") == "Yes" && Adjacent(user))
+	if(tgui_alert(user, question,name,list("Yes","No")) == "Yes" && Adjacent(user))
 		var/turf/T = find_safe_turf(zlevels=zlevels)
 
 		if(T)