tg Code complete, now to bugtest and clear compile errors.

code/modules/mob/living/brain/MMI.dm

@@ -64,6 +64,7 @@
 
 		brainmob.reset_perspective()
 		brain = newbrain
+		brain.organ_flags |= ORGAN_FROZEN
 
 		name = "Man-Machine Interface: [brainmob.real_name]"
 		update_icon()
@@ -100,6 +101,7 @@
 		user.put_in_hands(brain) //puts brain in the user's hand or otherwise drops it on the user's turf
 	else
 		brain.forceMove(get_turf(src))
+	brain.organ_flags &= ~ORGAN_FROZEN
 	brain = null //No more brain in here
 
 

code/modules/mob/living/carbon/alien/special/alien_embryo.dm

@@ -22,6 +22,7 @@
 	return S
 
 /obj/item/organ/body_egg/alien_embryo/on_life()
+	. = ..()
 	switch(stage)
 		if(2, 3)
 			if(prob(2))

code/modules/mob/living/carbon/damage_procs.dm

@@ -120,7 +120,10 @@
 /mob/living/carbon/adjustOrganLoss(slot, amount, maximum)
 	var/obj/item/organ/O = getorganslot(slot)
 	if(O && !(status_flags & GODMODE))
+		if(!maximum)
+			maximum = O.maxHealth
 		O.applyOrganDamage(amount, maximum)
+		O.onDamage(amount, maximum)
 
 /** setOrganLoss
   * inputs: slot (organ slot, like ORGAN_SLOT_HEART), amount(damage to be set to)
@@ -132,6 +135,7 @@
 	var/obj/item/organ/O = getorganslot(slot)
 	if(O && !(status_flags & GODMODE))
 		O.setOrganDamage(amount)
+		O.onSetDamage(amount)
 
 /** getOrganLoss
   * inputs: slot (organ slot, like ORGAN_SLOT_HEART)
@@ -143,6 +147,15 @@
 	if(O)
 		return O.damage
 
+/mob/living/carbon/adjustAllOrganLoss(amount, maximum)
+	for(var/o in internal_organs)
+		if(O && !(status_flags & GODMODE))
+			continue
+		if(!maximum)
+			maximum = O.maxHealth
+		O.applyOrganDamage(amount, maximum)
+		O.onDamage(amount, maximum)
+		
 
 ////////////////////////////////////////////
 

code/modules/mob/living/carbon/human/species_types/shadowpeople.dm

@@ -123,10 +123,8 @@
 	if(special != HEART_SPECIAL_SHADOWIFY)
 		blade = new/obj/item/light_eater
 		M.put_in_hands(blade)
-	START_PROCESSING(SSobj, src)
 
 /obj/item/organ/heart/nightmare/Remove(mob/living/carbon/M, special = 0)
-	STOP_PROCESSING(SSobj, src)
 	respawn_progress = 0
 	if(blade && special != HEART_SPECIAL_SHADOWIFY)
 		QDEL_NULL(blade)
@@ -139,9 +137,8 @@
 /obj/item/organ/heart/nightmare/update_icon()
 	return //always beating visually
 
-/obj/item/organ/heart/nightmare/process()
-	if(QDELETED(owner) || owner.stat != DEAD)
-		respawn_progress = 0
+/obj/item/organ/heart/nightmare/on_death()
+	if(!owner)
 		return
 	var/turf/T = get_turf(owner)
 	if(istype(T))

code/modules/mob/living/carbon/life.dm

@@ -8,8 +8,8 @@
 		damageoverlaytemp = 0
 		update_damage_hud()
 
-	if(stat != DEAD) //Reagent processing needs to come before breathing, to prevent edge cases.
-		handle_organs()
+	//Reagent processing needs to come before breathing, to prevent edge cases.
+	handle_organs()
 
 	. = ..()
 
@@ -384,9 +384,14 @@
 			. |= BP.on_life()
 
 /mob/living/carbon/proc/handle_organs()
-	for(var/V in internal_organs)
-		var/obj/item/organ/O = V
-		O.on_life()
+	if(stat != DEAD)
+		for(var/V in internal_organs)
+			var/obj/item/organ/O = V
+			O.on_life()
+	else
+		for(var/V in internal_organs)
+			var/obj/item/organ/O = V
+			O.on_death() //Needed so organs decay while inside the body.
 
 /mob/living/carbon/handle_diseases()
 	for(var/thing in diseases)