diff --git a/src/citra_qt/bootmanager.cpp b/src/citra_qt/bootmanager.cpp
index 1e902a8b662d7fdb7b5459b21af87ebf78c6a277..4be410fe00c9238dfcdc9493f3bd4e9ad062b600 100644
--- a/src/citra_qt/bootmanager.cpp
+++ b/src/citra_qt/bootmanager.cpp
@@ -87,8 +87,8 @@ private:
     GRenderWindow* parent;
 };
 
-GRenderWindow::GRenderWindow(QWidget* parent, GMainWindow& main_window) :
-    QWidget(parent), main_window(main_window), keyboard_id(0) {
+GRenderWindow::GRenderWindow(QWidget* parent, EmuThread* emu_thread) :
+    QWidget(parent), emu_thread(emu_thread), keyboard_id(0) {
 
     std::string window_title = Common::StringFromFormat("Citra | %s-%s", Common::g_scm_branch, Common::g_scm_desc);
     setWindowTitle(QString::fromStdString(window_title));
@@ -129,7 +129,7 @@ void GRenderWindow::moveContext()
     // We need to move GL context to the swapping thread in Qt5
 #if QT_VERSION > QT_VERSION_CHECK(5, 0, 0)
     // If the thread started running, move the GL Context to the new thread. Otherwise, move it back.
-    auto thread = QThread::currentThread() == qApp->thread() ? main_window.GetEmuThread() : qApp->thread();
+    auto thread = (QThread::currentThread() == qApp->thread() && emu_thread != nullptr) ? emu_thread : qApp->thread();
     child->context()->moveToThread(thread);
 #endif
 }
@@ -272,3 +272,11 @@ void GRenderWindow::OnClientAreaResized(unsigned width, unsigned height)
 void GRenderWindow::OnMinimalClientAreaChangeRequest(const std::pair<unsigned,unsigned>& minimal_size) {
     setMinimumSize(minimal_size.first, minimal_size.second);
 }
+
+void GRenderWindow::OnEmulationStarted(EmuThread* emu_thread) {
+    this->emu_thread = emu_thread;
+}
+
+void GRenderWindow::OnEmulationStopped() {
+    emu_thread = nullptr;
+}
diff --git a/src/citra_qt/bootmanager.h b/src/citra_qt/bootmanager.h
index e9b3ea664a7a4fc65ac8915e3d6ef8400d250a46..e575221877a0dde6b812f36af5cf97a97ea48a18 100644
--- a/src/citra_qt/bootmanager.h
+++ b/src/citra_qt/bootmanager.h
@@ -22,6 +22,7 @@ class EmuThread : public QThread
     Q_OBJECT
 
 public:
+    EmuThread(GRenderWindow* render_window);
 
     /**
      * Start emulation (on new thread)
@@ -50,15 +51,14 @@ public:
     bool IsRunning() { return running; }
 
     /**
-     * Shutdown (permanently stops) the emulation thread
+     * Requests for the emulation thread to stop running and shutdown emulation
      */
-    void Shutdown() { stop_run = true; };
+    void RequestShutdown() {
+        stop_run = true;
+        running = false;
+    };
 
 private:
-    friend class GMainWindow;
-
-    EmuThread(GRenderWindow* render_window);
-
     bool exec_step;
     bool running;
     std::atomic<bool> stop_run;
@@ -86,7 +86,7 @@ class GRenderWindow : public QWidget, public EmuWindow
     Q_OBJECT
 
 public:
-    GRenderWindow(QWidget* parent, GMainWindow& main_window);
+    GRenderWindow(QWidget* parent, EmuThread* emu_thread);
 
     // EmuWindow implementation
     void SwapBuffers() override;
@@ -115,6 +115,9 @@ public:
 public slots:
     void moveContext();  // overridden
 
+    void OnEmulationStarted(EmuThread* emu_thread);
+    void OnEmulationStopped();
+
 private:
     void OnMinimalClientAreaChangeRequest(const std::pair<unsigned,unsigned>& minimal_size) override;
 
@@ -122,8 +125,8 @@ private:
 
     QByteArray geometry;
 
-    GMainWindow& main_window;
-
     /// Device id of keyboard for use with KeyMap
     int keyboard_id;
+
+    EmuThread* emu_thread;
 };
diff --git a/src/citra_qt/debugger/disassembler.cpp b/src/citra_qt/debugger/disassembler.cpp
index f9423e1d63600e305444e53c4b007dd2811b5714..6400bb8560dc102e82fc0e0a59f5270e7fa6c26e 100644
--- a/src/citra_qt/debugger/disassembler.cpp
+++ b/src/citra_qt/debugger/disassembler.cpp
@@ -4,7 +4,6 @@
 
 #include "disassembler.h"
 
-#include "../main.h"
 #include "../bootmanager.h"
 #include "../hotkeys.h"
 
@@ -19,8 +18,8 @@
 #include "core/arm/disassembler/arm_disasm.h"
 
 
-DisassemblerModel::DisassemblerModel(QObject* parent) : QAbstractListModel(parent), base_address(0), code_size(0), program_counter(0), selection(QModelIndex()) {
-
+DisassemblerModel::DisassemblerModel(QObject* parent) :
+    QAbstractListModel(parent), base_address(0), code_size(0), program_counter(0), selection(QModelIndex()) {
 }
 
 int DisassemblerModel::columnCount(const QModelIndex& parent) const {
@@ -159,35 +158,28 @@ void DisassemblerModel::SetNextInstruction(unsigned int address) {
     emit dataChanged(prev_index, prev_index);
 }
 
-DisassemblerWidget::DisassemblerWidget(QWidget* parent, GMainWindow& main_window) :
-    QDockWidget(parent), main_window(main_window), base_addr(0) {
+DisassemblerWidget::DisassemblerWidget(QWidget* parent, EmuThread* emu_thread) :
+    QDockWidget(parent), emu_thread(emu_thread), base_addr(0) {
 
     disasm_ui.setupUi(this);
 
-    model = new DisassemblerModel(this);
-    disasm_ui.treeView->setModel(model);
-
     RegisterHotkey("Disassembler", "Start/Stop", QKeySequence(Qt::Key_F5), Qt::ApplicationShortcut);
     RegisterHotkey("Disassembler", "Step", QKeySequence(Qt::Key_F10), Qt::ApplicationShortcut);
     RegisterHotkey("Disassembler", "Step into", QKeySequence(Qt::Key_F11), Qt::ApplicationShortcut);
     RegisterHotkey("Disassembler", "Set Breakpoint", QKeySequence(Qt::Key_F9), Qt::ApplicationShortcut);
 
-    connect(disasm_ui.button_breakpoint, SIGNAL(clicked()), model, SLOT(OnSetOrUnsetBreakpoint()));
     connect(disasm_ui.button_step, SIGNAL(clicked()), this, SLOT(OnStep()));
     connect(disasm_ui.button_pause, SIGNAL(clicked()), this, SLOT(OnPause()));
     connect(disasm_ui.button_continue, SIGNAL(clicked()), this, SLOT(OnContinue()));
 
-    connect(disasm_ui.treeView->selectionModel(), SIGNAL(currentChanged(const QModelIndex&, const QModelIndex&)),
-            model, SLOT(OnSelectionChanged(const QModelIndex&)));
-
     connect(GetHotkey("Disassembler", "Start/Stop", this), SIGNAL(activated()), this, SLOT(OnToggleStartStop()));
     connect(GetHotkey("Disassembler", "Step", this), SIGNAL(activated()), this, SLOT(OnStep()));
     connect(GetHotkey("Disassembler", "Step into", this), SIGNAL(activated()), this, SLOT(OnStepInto()));
-    connect(GetHotkey("Disassembler", "Set Breakpoint", this), SIGNAL(activated()), model, SLOT(OnSetOrUnsetBreakpoint()));
+
+    setEnabled(false);
 }
 
-void DisassemblerWidget::Init()
-{
+void DisassemblerWidget::Init() {
     model->ParseFromAddress(Core::g_app_core->GetPC());
 
     disasm_ui.treeView->resizeColumnToContents(0);
@@ -199,25 +191,21 @@ void DisassemblerWidget::Init()
     disasm_ui.treeView->selectionModel()->setCurrentIndex(model_index, QItemSelectionModel::SelectCurrent | QItemSelectionModel::Rows);
 }
 
-void DisassemblerWidget::OnContinue()
-{
-    main_window.GetEmuThread()->SetRunning(true);
+void DisassemblerWidget::OnContinue() {
+    emu_thread->SetRunning(true);
 }
 
-void DisassemblerWidget::OnStep()
-{
+void DisassemblerWidget::OnStep() {
     OnStepInto(); // change later
 }
 
-void DisassemblerWidget::OnStepInto()
-{
-    main_window.GetEmuThread()->SetRunning(false);
-    main_window.GetEmuThread()->ExecStep();
+void DisassemblerWidget::OnStepInto() {
+    emu_thread->SetRunning(false);
+    emu_thread->ExecStep();
 }
 
-void DisassemblerWidget::OnPause()
-{
-    main_window.GetEmuThread()->SetRunning(false);
+void DisassemblerWidget::OnPause() {
+    emu_thread->SetRunning(false);
 
     // TODO: By now, the CPU might not have actually stopped...
     if (Core::g_app_core) {
@@ -225,17 +213,15 @@ void DisassemblerWidget::OnPause()
     }
 }
 
-void DisassemblerWidget::OnToggleStartStop()
-{
-    main_window.GetEmuThread()->SetRunning(!main_window.GetEmuThread()->IsRunning());
+void DisassemblerWidget::OnToggleStartStop() {
+    emu_thread->SetRunning(!emu_thread->IsRunning());
 }
 
-void DisassemblerWidget::OnDebugModeEntered()
-{
+void DisassemblerWidget::OnDebugModeEntered() {
     ARMword next_instr = Core::g_app_core->GetPC();
 
     if (model->GetBreakPoints().IsAddressBreakPoint(next_instr))
-        main_window.GetEmuThread()->SetRunning(false);
+        emu_thread->SetRunning(false);
 
     model->SetNextInstruction(next_instr);
 
@@ -244,16 +230,35 @@ void DisassemblerWidget::OnDebugModeEntered()
     disasm_ui.treeView->selectionModel()->setCurrentIndex(model_index, QItemSelectionModel::SelectCurrent | QItemSelectionModel::Rows);
 }
 
-void DisassemblerWidget::OnDebugModeLeft()
-{
-
+void DisassemblerWidget::OnDebugModeLeft() {
 }
 
-int DisassemblerWidget::SelectedRow()
-{
+int DisassemblerWidget::SelectedRow() {
     QModelIndex index = disasm_ui.treeView->selectionModel()->currentIndex();
     if (!index.isValid())
         return -1;
 
     return disasm_ui.treeView->selectionModel()->currentIndex().row();
 }
+
+void DisassemblerWidget::OnEmulationStarted(EmuThread* emu_thread) {
+    this->emu_thread = emu_thread;
+
+    model = new DisassemblerModel(this);
+    disasm_ui.treeView->setModel(model);
+
+    connect(disasm_ui.treeView->selectionModel(), SIGNAL(currentChanged(const QModelIndex&, const QModelIndex&)),
+        model, SLOT(OnSelectionChanged(const QModelIndex&)));
+    connect(disasm_ui.button_breakpoint, SIGNAL(clicked()), model, SLOT(OnSetOrUnsetBreakpoint()));
+    connect(GetHotkey("Disassembler", "Set Breakpoint", this), SIGNAL(activated()), model, SLOT(OnSetOrUnsetBreakpoint()));
+
+    Init();
+    setEnabled(true);
+}
+
+void DisassemblerWidget::OnEmulationStopped() {
+    disasm_ui.treeView->setModel(nullptr);
+    delete model;
+    emu_thread = nullptr;
+    setEnabled(false);
+}
diff --git a/src/citra_qt/debugger/disassembler.h b/src/citra_qt/debugger/disassembler.h
index d9e32dbdf5395add28eb0d1500fa0f38f94351bc..b771e95b742350905e49ba935fbf0a271c40d136 100644
--- a/src/citra_qt/debugger/disassembler.h
+++ b/src/citra_qt/debugger/disassembler.h
@@ -13,7 +13,7 @@
 #include "common/break_points.h"
 
 class QAction;
-class GMainWindow;
+class EmuThread;
 
 class DisassemblerModel : public QAbstractListModel
 {
@@ -51,7 +51,7 @@ class DisassemblerWidget : public QDockWidget
     Q_OBJECT
 
 public:
-    DisassemblerWidget(QWidget* parent, GMainWindow& main_window);
+    DisassemblerWidget(QWidget* parent, EmuThread* emu_thread);
 
     void Init();
 
@@ -65,6 +65,9 @@ public slots:
     void OnDebugModeEntered();
     void OnDebugModeLeft();
 
+    void OnEmulationStarted(EmuThread* emu_thread);
+    void OnEmulationStopped();
+
 private:
     // returns -1 if no row is selected
     int SelectedRow();
@@ -75,5 +78,5 @@ private:
 
     u32 base_addr;
 
-    GMainWindow& main_window;
+    EmuThread* emu_thread;
 };
diff --git a/src/citra_qt/main.cpp b/src/citra_qt/main.cpp
index dd180baa4be9d81341b80b7848df4746b2b2aba4..7de2bf8ba92bc177c8c19f456245f1e42cd848de 100644
--- a/src/citra_qt/main.cpp
+++ b/src/citra_qt/main.cpp
@@ -15,6 +15,7 @@
 #include "common/logging/log.h"
 #include "common/logging/backend.h"
 #include "common/logging/filter.h"
+#include "common/make_unique.h"
 #include "common/platform.h"
 #include "common/scope_exit.h"
 
@@ -55,14 +56,14 @@ GMainWindow::GMainWindow() : emu_thread(nullptr)
     ui.setupUi(this);
     statusBar()->hide();
 
-    render_window = new GRenderWindow(this, *this);
+    render_window = new GRenderWindow(this, emu_thread.get());
     render_window->hide();
 
     profilerWidget = new ProfilerWidget(this);
     addDockWidget(Qt::BottomDockWidgetArea, profilerWidget);
     profilerWidget->hide();
 
-    disasmWidget = new DisassemblerWidget(this, *this);
+    disasmWidget = new DisassemblerWidget(this, emu_thread.get());
     addDockWidget(Qt::BottomDockWidgetArea, disasmWidget);
     disasmWidget->hide();
 
@@ -138,14 +139,10 @@ GMainWindow::GMainWindow() : emu_thread(nullptr)
     connect(ui.action_Single_Window_Mode, SIGNAL(triggered(bool)), this, SLOT(ToggleWindowMode()));
     connect(ui.action_Hotkeys, SIGNAL(triggered()), this, SLOT(OnOpenHotkeysDialog()));
 
-    // BlockingQueuedConnection is important here, it makes sure we've finished refreshing our views before the CPU continues
-    connect(emu_thread, SIGNAL(DebugModeEntered()), disasmWidget, SLOT(OnDebugModeEntered()), Qt::BlockingQueuedConnection);
-    connect(emu_thread, SIGNAL(DebugModeEntered()), registersWidget, SLOT(OnDebugModeEntered()), Qt::BlockingQueuedConnection);
-    connect(emu_thread, SIGNAL(DebugModeEntered()), callstackWidget, SLOT(OnDebugModeEntered()), Qt::BlockingQueuedConnection);
-
-    connect(emu_thread, SIGNAL(DebugModeLeft()), disasmWidget, SLOT(OnDebugModeLeft()), Qt::BlockingQueuedConnection);
-    connect(emu_thread, SIGNAL(DebugModeLeft()), registersWidget, SLOT(OnDebugModeLeft()), Qt::BlockingQueuedConnection);
-    connect(emu_thread, SIGNAL(DebugModeLeft()), callstackWidget, SLOT(OnDebugModeLeft()), Qt::BlockingQueuedConnection);
+    connect(this, SIGNAL(EmulationStarted(EmuThread*)), disasmWidget, SLOT(OnEmulationStarted(EmuThread*)));
+    connect(this, SIGNAL(EmulationStopped()), disasmWidget, SLOT(OnEmulationStopped()));
+    connect(this, SIGNAL(EmulationStarted(EmuThread*)), render_window, SLOT(OnEmulationStarted(EmuThread*)));
+    connect(this, SIGNAL(EmulationStopped()), render_window, SLOT(OnEmulationStopped()));
 
     // Setup hotkeys
     RegisterHotkey("Main Window", "Load File", QKeySequence::Open);
@@ -199,35 +196,62 @@ void GMainWindow::OnDisplayTitleBars(bool show)
 void GMainWindow::BootGame(std::string filename) {
     LOG_INFO(Frontend, "Citra starting...\n");
 
+    // Initialize the core emulation
     System::Init(render_window);
 
-    // Load a game or die...
+    // Load the game
     if (Loader::ResultStatus::Success != Loader::LoadFile(filename)) {
         LOG_CRITICAL(Frontend, "Failed to load ROM!");
+        System::Shutdown();
+        return;
     }
 
-    disasmWidget->Init();
-    registersWidget->OnDebugModeEntered();
-    callstackWidget->OnDebugModeEntered();
-
-    emu_thread = new EmuThread(render_window);
+    // Create and start the emulation thread
+    emu_thread = Common::make_unique<EmuThread>(render_window);
+    emit EmulationStarted(emu_thread.get());
     emu_thread->start();
 
+    // BlockingQueuedConnection is important here, it makes sure we've finished refreshing our views before the CPU continues
+    connect(emu_thread.get(), SIGNAL(DebugModeEntered()), disasmWidget, SLOT(OnDebugModeEntered()), Qt::BlockingQueuedConnection);
+    connect(emu_thread.get(), SIGNAL(DebugModeEntered()), registersWidget, SLOT(OnDebugModeEntered()), Qt::BlockingQueuedConnection);
+    connect(emu_thread.get(), SIGNAL(DebugModeEntered()), callstackWidget, SLOT(OnDebugModeEntered()), Qt::BlockingQueuedConnection);
+    connect(emu_thread.get(), SIGNAL(DebugModeLeft()), disasmWidget, SLOT(OnDebugModeLeft()), Qt::BlockingQueuedConnection);
+    connect(emu_thread.get(), SIGNAL(DebugModeLeft()), registersWidget, SLOT(OnDebugModeLeft()), Qt::BlockingQueuedConnection);
+    connect(emu_thread.get(), SIGNAL(DebugModeLeft()), callstackWidget, SLOT(OnDebugModeLeft()), Qt::BlockingQueuedConnection);
+
+    // Update the GUI
+    registersWidget->OnDebugModeEntered();
+    callstackWidget->OnDebugModeEntered();
     render_window->show();
+
     OnStartGame();
 }
 
 void GMainWindow::ShutdownGame() {
-    // Shutdown the emulation thread and wait for it to complete
-    emu_thread->SetRunning(false);
-    emu_thread->Shutdown();
-    emu_thread->wait();
-    delete emu_thread;
-    emu_thread = nullptr;
+    // Shutdown the emulation thread
+    emu_thread->RequestShutdown();
+
+    // Disconnect signals that are attached to the current emulation thread
+    disconnect(emu_thread.get(), SIGNAL(DebugModeEntered()), disasmWidget, SLOT(OnDebugModeEntered()));
+    disconnect(emu_thread.get(), SIGNAL(DebugModeEntered()), registersWidget, SLOT(OnDebugModeEntered()));
+    disconnect(emu_thread.get(), SIGNAL(DebugModeEntered()), callstackWidget, SLOT(OnDebugModeEntered()));
+    disconnect(emu_thread.get(), SIGNAL(DebugModeLeft()), disasmWidget, SLOT(OnDebugModeLeft()));
+    disconnect(emu_thread.get(), SIGNAL(DebugModeLeft()), registersWidget, SLOT(OnDebugModeLeft()));
+    disconnect(emu_thread.get(), SIGNAL(DebugModeLeft()), callstackWidget, SLOT(OnDebugModeLeft()));
 
     // Release emu threads from any breakpoints
+    // This belongs after RequestShutdown() and before wait() because if emulation stops on a GPU
+    // breakpoint after (or before) RequestShutdown() is called, the emulation would never be able
+    // to continue out to the main loop and terminate. Thus wait() would hang forever.
+    // TODO(bunnei): This function is not thread safe, but it's being used as if it were
     Pica::g_debug_context->ClearBreakpoints();
 
+    emit EmulationStopped();
+
+    // Wait for emulation thread to complete and delete it
+    emu_thread->wait();
+    emu_thread = nullptr;
+
     // Shutdown the core emulation
     System::Shutdown();
 
diff --git a/src/citra_qt/main.h b/src/citra_qt/main.h
index 1821ae35fe008e11be284ed82ccb98e24a05b273..3e29534fbc384e61d35f65df3071b9c94609dc5b 100644
--- a/src/citra_qt/main.h
+++ b/src/citra_qt/main.h
@@ -5,6 +5,7 @@
 #ifndef _CITRA_QT_MAIN_HXX_
 #define _CITRA_QT_MAIN_HXX_
 
+#include <memory>
 #include <QMainWindow>
 
 #include "ui_main.h"
@@ -35,9 +36,23 @@ public:
     GMainWindow();
     ~GMainWindow();
 
-    EmuThread* GetEmuThread() {
-        return emu_thread;
-    }
+signals:
+
+    /**
+     * Signal that is emitted when a new EmuThread has been created and an emulation session is
+     * about to start. At this time, the core system emulation has been initialized, and all
+     * emulation handles and memory should be valid.
+     *
+     * @param emu_thread Pointer to the newly created EmuThread (to be used by widgets that need to
+     *      access/change emulation state).
+     */
+    void EmulationStarting(EmuThread* emu_thread);
+
+    /**
+     * Signal that is emitted when emulation is about to stop. At this time, the EmuThread and core
+     * system emulation handles and memory are still valid, but are about become invalid.
+     */
+    void EmulationStopping();
 
 private:
     void BootGame(std::string filename);
@@ -60,7 +75,8 @@ private:
     Ui::MainWindow ui;
 
     GRenderWindow* render_window;
-    EmuThread* emu_thread;
+
+    std::unique_ptr<EmuThread> emu_thread;
 
     ProfilerWidget* profilerWidget;
     DisassemblerWidget* disasmWidget;