diff --git a/ArduCopter/ArduCopter.pde b/ArduCopter/ArduCopter.pde
index 3c2054bdb4..d0a2ce6f5e 100644
--- a/ArduCopter/ArduCopter.pde
+++ b/ArduCopter/ArduCopter.pde
@@ -108,6 +108,7 @@
 #include <AP_InertialSensor.h>  // ArduPilot Mega Inertial Sensor (accel & gyro) Library
 #include <AP_AHRS.h>
 #include <AP_NavEKF.h>
+#include <AP_Mission.h>         // Mission command library
 #include <AC_PID.h>             // PID library
 #include <AC_P.h>               // P library
 #include <AC_AttitudeControl.h> // Attitude control library
@@ -347,6 +348,13 @@ AP_AHRS_NavEKF ahrs(ins, barometer, g_gps);
 AP_AHRS_DCM ahrs(ins, barometer, g_gps);
 #endif
 
+// Mission library
+// forward declaration to keep compiler happy
+static bool start_command(const AP_Mission::Mission_Command& cmd);
+static bool verify_command(const AP_Mission::Mission_Command& cmd);
+static void exit_mission();
+AP_Mission mission(&start_command, &verify_command, &exit_mission);
+
 ////////////////////////////////////////////////////////////////////////////////
 // Optical flow sensor
 ////////////////////////////////////////////////////////////////////////////////
@@ -514,18 +522,6 @@ static int32_t home_bearing;
 static int32_t home_distance;
 // distance between plane and next waypoint in cm.
 static uint32_t wp_distance;
-// Register containing the index of the current navigation command in the mission script
-static int16_t command_nav_index;
-// Register containing the index of the previous navigation command in the mission script
-// Used to manage the execution of conditional commands
-static uint8_t prev_nav_index;
-// Register containing the index of the current conditional command in the mission script
-static uint8_t command_cond_index;
-// Used to track the required WP navigation information
-// options include
-// NAV_ALTITUDE - have we reached the desired altitude?
-// NAV_LOCATION - have we reached the desired location?
-// NAV_DELAY    - have we waited at the waypoint the desired time?
 static float lon_error, lat_error;      // Used to report how many cm we are from the next waypoint or loiter target position
 static uint8_t land_state;              // records state of land (flying to location, descending)
 
@@ -580,14 +576,6 @@ static uint16_t loiter_time_max;                // How long we should stay in Lo
 static uint32_t loiter_time;                    // How long have we been loitering - The start time in millis
 
 
-////////////////////////////////////////////////////////////////////////////////
-// CH7 and CH8 save waypoint control
-////////////////////////////////////////////////////////////////////////////////
-// This register tracks the current Mission Command index when writing
-// a mission using Ch7 or Ch8 aux switches in flight
-static int8_t aux_switch_wp_index;
-
-
 ////////////////////////////////////////////////////////////////////////////////
 // Battery Sensors
 ////////////////////////////////////////////////////////////////////////////////
@@ -614,10 +602,6 @@ static const struct  Location &home = ahrs.get_home();
 
 // Current location of the copter
 static struct   Location current_loc;
-// Holds the current loaded command from the EEPROM for navigation
-static struct   Location command_nav_queue;
-// Holds the current loaded command from the EEPROM for conditional scripts
-static struct   Location command_cond_queue;
 
 
 ////////////////////////////////////////////////////////////////////////////////