diff --git a/code/controllers/subsystem/atoms.dm b/code/controllers/subsystem/atoms.dm
index 40841f30f04..4e4543388c8 100644
--- a/code/controllers/subsystem/atoms.dm
+++ b/code/controllers/subsystem/atoms.dm
@@ -14,17 +14,22 @@ SUBSYSTEM_DEF(atoms)
 
 	var/list/BadInitializeCalls = list()
 
+	initialized = INITIALIZATION_INSSATOMS
+
 /datum/controller/subsystem/atoms/Initialize(timeofday)
 	GLOB.fire_overlay.appearance_flags = RESET_COLOR
 	setupGenetics() //to set the mutations' sequence
+
 	initialized = INITIALIZATION_INNEW_MAPLOAD
 	InitializeAtoms()
+	initialized = INITIALIZATION_INNEW_REGULAR
 	return ..()
 
 /datum/controller/subsystem/atoms/proc/InitializeAtoms(list/atoms)
 	if(initialized == INITIALIZATION_INSSATOMS)
 		return
 
+	old_initialized = initialized
 	initialized = INITIALIZATION_INNEW_MAPLOAD
 
 	var/count
@@ -47,7 +52,7 @@ SUBSYSTEM_DEF(atoms)
 	testing("Initialized [count] atoms")
 	pass(count)
 
-	initialized = INITIALIZATION_INNEW_REGULAR
+	initialized = old_initialized
 
 	if(late_loaders.len)
 		for(var/I in late_loaders)
diff --git a/code/modules/mapping/map_template.dm b/code/modules/mapping/map_template.dm
index 9faa709c0b1..1f3472c7ba5 100644
--- a/code/modules/mapping/map_template.dm
+++ b/code/modules/mapping/map_template.dm
@@ -55,8 +55,9 @@
 				atmos_machines += A
 
 	SSmapping.reg_in_areas_in_z(areas)
-	SSatoms.InitializeAtoms(turfs)
-	SSatoms.InitializeAtoms(atoms)
+	SSatoms.InitializeAtoms(areas + turfs + atoms)
+	// NOTE, now that Initialize and LateInitialize run correctly, do we really
+	// need these two below?
 	SSmachines.setup_template_powernets(cables)
 	SSair.setup_template_machinery(atmos_machines)