diff --git a/scripts/microbe_stage/microbe_replacement.lua b/scripts/microbe_stage/microbe_replacement.lua
index f5445af14e2..62ab40ba5c5 100644
--- a/scripts/microbe_stage/microbe_replacement.lua
+++ b/scripts/microbe_stage/microbe_replacement.lua
@@ -11,6 +11,7 @@ end
 function MicrobeReplacementSystem:activate()
     activeCreatureId = Engine:playerData():activeCreature()
     if Engine:playerData():isBoolSet("edited_microbe") then
+        Engine:playerData():setBool("edited_microbe", false);
         workingMicrobe = Microbe(Entity(activeCreatureId, GameState.MICROBE_EDITOR))
         if workingMicrobe:getCompoundAmount(CompoundRegistry.getCompoundId("atp")) == 0 then
             workingMicrobe:storeCompound(CompoundRegistry.getCompoundId("atp"), 10)
diff --git a/src/engine/engine.cpp b/src/engine/engine.cpp
index 2b09b416e8c..9d17616cb55 100644
--- a/src/engine/engine.cpp
+++ b/src/engine/engine.cpp
@@ -61,6 +61,7 @@
 #include <OgreWindowEventUtilities.h>
 #include <OISInputManager.h>
 #include <OISMouse.h>
+#include <map>
 #include <random>
 #include <set>
 #include <stdlib.h>
@@ -83,7 +84,9 @@ struct Engine::Implementation : public Ogre::WindowEventListener {
         Engine& engine
     ) : m_engine(engine),
         m_rng(),
-        m_playerData("player")
+        m_playerData("player"),
+        m_nextShutdownSystems(new std::map<System*, int>),
+        m_prevShutdownSystems(new std::map<System*, int>)
     {
     }
 
@@ -413,6 +416,9 @@ struct Engine::Implementation : public Ogre::WindowEventListener {
 
     bool m_quitRequested = false;
 
+    std::map<System*, int>* m_nextShutdownSystems;
+    std::map<System*, int>* m_prevShutdownSystems;
+
     struct Graphics {
 
         std::unique_ptr<Ogre::Root> root;
@@ -488,6 +494,8 @@ Engine::luaBindings() {
         .def("load", &Engine::load)
         .def("save", &Engine::save)
         .def("quit", &Engine::quit)
+        .def("timedSystemShutdown", &Engine::timedSystemShutdown)
+        .def("isSystemTimedShutdown", &Engine::isSystemTimedShutdown)
         .property("componentFactory", &Engine::componentFactory)
         .property("keyboard", &Engine::keyboard)
         .property("mouse", &Engine::mouse)
@@ -640,6 +648,13 @@ Engine::setCurrentGameState(
 ) {
     assert(gameState != nullptr && "GameState must not be null");
     m_impl->m_nextGameState = gameState;
+    for (auto& pair : *m_impl->m_prevShutdownSystems){
+        //Make sure systems are deactivated before any potential reactivations
+        pair.first->deactivate();
+    }
+    m_impl->m_prevShutdownSystems = m_impl->m_nextShutdownSystems;
+    m_impl->m_nextShutdownSystems = m_impl->m_prevShutdownSystems;
+    m_impl->m_nextShutdownSystems->clear();
 }
 
 PlayerData&
@@ -710,8 +725,36 @@ Engine::update(
     }
     assert(m_impl->m_currentGameState != nullptr);
     m_impl->m_currentGameState->update(milliseconds);
+    // Update any timed shutdown systems
+    auto itr = m_impl->m_prevShutdownSystems->begin();
+    while (itr != m_impl->m_prevShutdownSystems->end()) {
+        int updateTime = std::min(itr->second, milliseconds);
+        itr->first->update(updateTime);
+        itr->second = itr->second - updateTime;
+        if (itr->second == 0) {
+            // Remove systems that had timed out
+            itr->first->deactivate();
+            m_impl->m_prevShutdownSystems->erase(itr++);
+        } else {
+            ++itr;
+        }
+    }
     if (not m_impl->m_serialization.loadFile.empty()) {
         m_impl->loadSavegame();
     }
 }
 
+void
+Engine::timedSystemShutdown(
+    System& system,
+    int milliseconds
+) {
+    (*m_impl->m_nextShutdownSystems)[&system] = milliseconds;
+}
+
+bool
+Engine::isSystemTimedShutdown(
+    System& system
+) const {
+    return m_impl->m_prevShutdownSystems->find(&system) !=  m_impl->m_prevShutdownSystems->end();
+}
diff --git a/src/engine/engine.h b/src/engine/engine.h
index a93a3f04301..9125af5b945 100644
--- a/src/engine/engine.h
+++ b/src/engine/engine.h
@@ -64,6 +64,8 @@ class Engine {
     * - Engine::load()
     * - Engine::save()
     * - Engine::quit()
+    * - Engine::timedSystemShutdown()
+    * - Engine::isSystemTimedShutdown()
     * - Engine::componentFactory() (as property)
     * - Engine::keyboard() (as property)
     * - Engine::mouse() (as property)
@@ -270,11 +272,48 @@ class Engine {
         int milliseconds
     );
 
+    /**
+    * @brief Keeps a system alive after being shut down for a specified amount of  time
+    *
+    * Note that this causes update to be called for the specified duration so be careful
+    * to ensure that the system is not enabled or it will get update calls twice.
+    *
+    * @param system
+    *   The system to keep updated
+    *
+    * @param milliseconds
+    *   The number of milliseconds to keep the system updated for
+    */
+    void
+    timedSystemShutdown(
+        System& system,
+        int milliseconds
+    );
+
+    /**
+    * @brief Returns whether the specified system has already been set for a timed shutdown
+    *
+    * @param system
+    *   The system to check for
+    *
+    * @return
+    */
+    bool
+    isSystemTimedShutdown(
+        System& system
+    ) const;
+
     /**
     * @brief Transfers an entity from one gamestate to another
     *
+    * @param oldEntityId
+    *  The id of the entity to transfer in the old entitymanager
     *
+    * @param oldEntityManager
+    *  The old entitymanager which is currently handling the entity
     *
+    * @param newGameState
+    *  The new gamestate to transfer the entity to
     */
     EntityId
     transferEntityGameState(
diff --git a/src/engine/entity_filter.cpp b/src/engine/entity_filter.cpp
index 200798d5d13..8b33d6447c3 100644
--- a/src/engine/entity_filter.cpp
+++ b/src/engine/entity_filter.cpp
@@ -288,6 +288,11 @@ EntityFilter<ComponentTypes...>::removedEntities() {
     return m_impl->m_removedEntities;
 }
 
+template<typename... ComponentTypes>
+EntityManager*
+EntityFilter<ComponentTypes...>::entityManager() {
+    return m_impl->m_entityManager;
+}
 
 template<typename... ComponentTypes>
 void
diff --git a/src/engine/entity_filter.h b/src/engine/entity_filter.h
index cd6331c8b81..44b748f4c21 100644
--- a/src/engine/entity_filter.h
+++ b/src/engine/entity_filter.h
@@ -211,6 +211,14 @@ class EntityFilter {
     std::unordered_set<EntityId>&
     removedEntities();
 
+    /** 
+    * @brief Gets the current entiyManager
+    *
+    * @return
+    */
+    EntityManager*
+    entityManager();
+    
     /**
     * @brief Sets the entity manager this filter applies to
     *
diff --git a/src/sound/sound_source_system.cpp b/src/sound/sound_source_system.cpp
index 6b55ccce812..21f2d7518fb 100644
--- a/src/sound/sound_source_system.cpp
+++ b/src/sound/sound_source_system.cpp
@@ -300,7 +300,7 @@ struct SoundSourceSystem::Implementation {
     removeSoundsForEntity(
         EntityId entityId
     ) {
-        EntityManager& entityManager = Game::instance().engine().currentGameState()->entityManager();
+        EntityManager& entityManager = *m_entities.entityManager();
         SoundSourceComponent* soundSource = static_cast<SoundSourceComponent*>(entityManager.getComponent(entityId, SoundSourceComponent::TYPE_ID));
         for (const auto& pair : soundSource->m_sounds) {
             Sound* sound = pair.second.get();
@@ -430,13 +430,16 @@ SoundSourceSystem::activate() {
 
 void
 SoundSourceSystem::deactivate() {
-    System::deactivate();
-    auto& soundManager = OgreOggSound::OgreOggSoundManager::getSingleton();
-    m_impl->removeAllSounds();
-    for (auto& value : m_impl->m_entities) {
-        std::get<0>(value.second)->m_ambientSoundCountdown = 0;
+    if (this->engine()->isSystemTimedShutdown(*this)) {
+        System::deactivate();
+        m_impl->removeAllSounds();
+    }
+    else {
+        for (auto& value : m_impl->m_entities) {
+            std::get<0>(value.second)->m_ambientSoundCountdown = 1500;
+        }
+        this->engine()->timedSystemShutdown(*this, 1500);
     }
-    soundManager.setSceneManager(nullptr);
 }