diff --git a/code/ai/ai.h b/code/ai/ai.h
index f5fc94b8a75..090204cc50f 100644
--- a/code/ai/ai.h
+++ b/code/ai/ai.h
@@ -276,8 +276,8 @@ typedef struct ai_info {
 	int		ai_class;				//	Class.  Might be override of default.
 
 	//	Probably become obsolete, to be replaced by path_start, path_cur, etc.
-	waypoint_list	*wp_list;		// waypoint list being followed
-	int				 wp_index;		// waypoint index in list
+	int		wp_list_index;			// index of waypoint list being followed
+	int		wp_index;				// index of waypoint in list
 	int		wp_flags;				//	waypoint flags, see WPF_xxxx
 	int		waypoint_speed_cap;		// -1 no cap, otherwise cap - changed to int by Goober5000
 
@@ -533,7 +533,7 @@ extern void ai_ignore_wing(object *ignorer, int wingnum);
 extern void ai_dock_with_object(object *docker, int docker_index, object *dockee, int dockee_index, int dock_type);
 extern void ai_stay_still(object *still_objp, vec3d *view_pos);
 extern void ai_do_default_behavior(object *obj);
-extern void ai_start_waypoints(object *objp, waypoint_list *wp_list, int wp_flags, int start_index);
+extern void ai_start_waypoints(object *objp, int wl_index, int wp_flags, int start_index);
 extern void ai_ship_hit(object *objp_ship, object *hit_objp, vec3d *hit_normal);
 extern void ai_ship_destroy(int shipnum);
 extern vec3d ai_get_acc_limit(vec3d* vel_limit, const object* objp);
diff --git a/code/ai/aicode.cpp b/code/ai/aicode.cpp
index 70161e5d503..6606cd7844a 100644
--- a/code/ai/aicode.cpp
+++ b/code/ai/aicode.cpp
@@ -3515,20 +3515,31 @@ void ai_dock_with_object(object *docker, int docker_index, object *dockee, int d
 //	flags tells:
 //		WPF_REPEAT		Set -> repeat waypoints.
 //		WPF_BACKTRACK	Go in reverse.
-void ai_start_waypoints(object *objp, waypoint_list *wp_list, int wp_flags, int start_index)
+void ai_start_waypoints(object *objp, int wp_list_index, int wp_flags, int start_index)
 {
-	ai_info	*aip;
-	Assert(wp_list != NULL);
+	if (Waypoint_lists.empty())
+	{
+		Warning(LOCATION, "No waypoint lists in mission!");
+		return;
+	}
 
-	if (start_index < 0 || start_index >= (int)wp_list->get_waypoints().size())
+	auto wp_list = find_waypoint_list_at_index(wp_list_index);
+	if (!wp_list)
+	{
+		Warning(LOCATION, "wp_list_index %d must be a valid waypoint list index!", wp_list_index);
+		wp_list_index = 0;
+	}
+
+	auto wp = find_waypoint_at_index(wp_list, start_index);
+	if (!wp)
 	{
 		Warning(LOCATION, "Starting index for %s on '%s' is out of range!", Ships[objp->instance].ship_name, wp_list->get_name());
 		start_index = (wp_flags & WPF_BACKTRACK) ? (int)wp_list->get_waypoints().size() - 1 : 0;
 	}
 
-	aip = &Ai_info[Ships[objp->instance].ai_index];
+	auto aip = &Ai_info[Ships[objp->instance].ai_index];
 
-	if ( (aip->mode == AIM_WAYPOINTS) && (aip->wp_list == wp_list) )
+	if ( (aip->mode == AIM_WAYPOINTS) && (aip->wp_list_index == wp_list_index) )
 	{
 		if (aip->wp_index == INVALID_WAYPOINT_POSITION)
 		{
@@ -3548,7 +3559,7 @@ void ai_start_waypoints(object *objp, waypoint_list *wp_list, int wp_flags, int
 	}
 	aip->ai_flags.remove(AI::AI_Flags::Formation_object);
 
-	aip->wp_list = wp_list;
+	aip->wp_list_index = wp_list_index;
 	aip->wp_index = start_index;
 	aip->wp_flags = wp_flags;
 	aip->mode = AIM_WAYPOINTS;
@@ -4896,19 +4907,20 @@ void ai_waypoints()
 
 	// sanity checking for stuff that should never happen
 	if (aip->wp_index == INVALID_WAYPOINT_POSITION) {
-		if (aip->wp_list == NULL) {
+		if (aip->wp_list_index < 0) {
 			UNREACHABLE("Waypoints should have been assigned already!");
-			ai_start_waypoints(Pl_objp, &Waypoint_lists.front(), WPF_REPEAT, 0);
+			ai_start_waypoints(Pl_objp, 0, WPF_REPEAT, 0);
 		} else {
 			UNREACHABLE("Waypoints should have been started already!");
-			ai_start_waypoints(Pl_objp, aip->wp_list, WPF_REPEAT, 0);
+			ai_start_waypoints(Pl_objp, aip->wp_list_index, WPF_REPEAT, 0);
 		}
 	}
 	
-	Assert(!aip->wp_list->get_waypoints().empty());	// What? Is this zero? Probably never got initialized!
+	auto wp_list = find_waypoint_list_at_index(aip->wp_list_index);
+	Assert(!wp_list->get_waypoints().empty());	// What? Is this zero? Probably never got initialized!
 
 	bool done, treat_as_ship;
-	ai_fly_to_target_position(aip->wp_list->get_waypoints()[aip->wp_index].get_pos(), &done, &treat_as_ship);
+	ai_fly_to_target_position(wp_list->get_waypoints()[aip->wp_index].get_pos(), &done, &treat_as_ship);
 
 	if ( done ) {
 		bool reached_end;
@@ -4918,7 +4930,7 @@ void ai_waypoints()
 			reached_end = (aip->wp_index == -1);
 		} else {
 			++aip->wp_index;
-			reached_end = (aip->wp_index == (int)aip->wp_list->get_waypoints().size());
+			reached_end = (aip->wp_index == static_cast<int>(wp_list->get_waypoints().size()));
 		}
 
 		if (reached_end) {
@@ -4926,7 +4938,7 @@ void ai_waypoints()
 			if ( aip->wp_flags & WPF_REPEAT ) {
 				 // go back to the start.
 				if (aip->wp_flags & WPF_BACKTRACK) {
-					aip->wp_index = (int)aip->wp_list->get_waypoints().size() - 1;
+					aip->wp_index = static_cast<int>(wp_list->get_waypoints().size() - 1);
 				} else {
 					aip->wp_index = 0;
 				}
@@ -4944,10 +4956,10 @@ void ai_waypoints()
 				// ai_fly_to_target_position when it marks the AI directive as complete
 				if ( treat_as_ship ) {
 					ai_mission_goal_complete( aip );					// this call should reset the AI mode
-					mission_log_add_entry( LOG_WAYPOINTS_DONE, Ships[Pl_objp->instance].ship_name, aip->wp_list->get_name(), -1 );
+					mission_log_add_entry( LOG_WAYPOINTS_DONE, Ships[Pl_objp->instance].ship_name, wp_list->get_name(), -1 );
 				} else {
 					ai_mission_wing_goal_complete( Ships[Pl_objp->instance].wingnum, &(aip->goals[aip->active_goal]) );
-					mission_log_add_entry( LOG_WAYPOINTS_DONE, Wings[Ships[Pl_objp->instance].wingnum].name, aip->wp_list->get_name(), -1 );
+					mission_log_add_entry( LOG_WAYPOINTS_DONE, Wings[Ships[Pl_objp->instance].wingnum].name, wp_list->get_name(), -1 );
 				}
 				// adds scripting hook for 'On Waypoints Done' --wookieejedi
 				if (scripting::hooks::OnWaypointsDone->isActive()) {
@@ -4955,7 +4967,7 @@ void ai_waypoints()
 						scripting::hook_param_list(
 							scripting::hook_param("Ship", 'o', Pl_objp),
 							scripting::hook_param("Wing", 'o', scripting::api::l_Wing.Set(Ships[Pl_objp->instance].wingnum)),
-							scripting::hook_param("Waypointlist", 'o', scripting::api::l_WaypointList.Set(scripting::api::waypointlist_h(aip->wp_list)))
+							scripting::hook_param("Waypointlist", 'o', scripting::api::l_WaypointList.Set(scripting::api::waypointlist_h(wp_list)))
 						));
 				}
 			}
@@ -12665,7 +12677,7 @@ int ai_formation()
 			// skip if wing leader has no waypoint order or a different waypoint list
 			// ...or if it's a different start index or direction
 			if (    (laip->mode != AIM_WAYPOINTS)
-				||  (laip->wp_list != aip->wp_list)
+				||  (laip->wp_list_index != aip->wp_list_index)
 				||  (laip->submode_parm0 != aip->submode_parm0)
 				|| ((laip->wp_flags & WPF_BACKTRACK) != (aip->wp_flags & WPF_BACKTRACK))
 				) {
@@ -12673,16 +12685,17 @@ int ai_formation()
 			}
 		}
 
-		aip->wp_list = laip->wp_list;
+		aip->wp_list_index = laip->wp_list_index;
 		aip->wp_index = laip->wp_index;
 		aip->wp_flags = laip->wp_flags;
 
-		if (aip->wp_list != nullptr) {
+		auto wp_list = find_waypoint_list_at_index(aip->wp_list_index);
+		if (wp_list) {
 			if (aip->wp_flags & WPF_BACKTRACK) {
 				if (aip->wp_index == -1)
 					++aip->wp_index;
 			} else {
-				if (aip->wp_index == (int)aip->wp_list->get_waypoints().size())
+				if (aip->wp_index == static_cast<int>(wp_list->get_waypoints().size()))
 					--aip->wp_index;
 			}
 		}
@@ -15455,7 +15468,7 @@ void init_ai_object(int objnum)
 	//Init stuff from AI class and AI profiles
 	init_aip_from_class_and_profile(aip, &Ai_classes[Ship_info[ship_type].ai_class], The_mission.ai_profile);
 
-	aip->wp_list = NULL;
+	aip->wp_list_index = INVALID_WAYPOINT_POSITION;
 	aip->wp_index = INVALID_WAYPOINT_POSITION;
 
 	aip->attacker_objnum = -1;
diff --git a/code/ai/aigoals.cpp b/code/ai/aigoals.cpp
index d81076df70d..4953b42fc82 100644
--- a/code/ai/aigoals.cpp
+++ b/code/ai/aigoals.cpp
@@ -166,7 +166,7 @@ void ai_goal_reset(ai_goal *aigp, bool adding_goal, int ai_mode, int ai_submode,
 	aigp->target_name = nullptr;
 	aigp->target_name_index = -1;
 
-	aigp->wp_list = nullptr;
+	aigp->wp_list_index = -1;
 
 	aigp->target_instance = -1;
 	aigp->target_signature = -1;
@@ -738,8 +738,8 @@ void ai_add_goal_sub_player(int type, int mode, int submode, const char *target_
 
 	if ( mode == AI_GOAL_WARP ) {
 		if (submode >= 0) {
-			aigp->wp_list = find_waypoint_list_at_index(submode);
-			Assert(aigp->wp_list != NULL);
+			aigp->wp_list_index = submode;
+			Assert(find_waypoint_list_at_index(aigp->wp_list_index) != nullptr);
 		}
 	}
 
@@ -1605,10 +1605,10 @@ ai_achievability ai_mission_goal_achievable( int objnum, ai_goal *aigp )
 	// check to see if we have a valid list.  If not, then try to set one up.  If that
 	// fails, then we must pitch this order
 	if ( (aigp->ai_mode == AI_GOAL_WAYPOINTS_ONCE) || (aigp->ai_mode == AI_GOAL_WAYPOINTS) ) {
-		if ( aigp->wp_list == NULL ) {
-			aigp->wp_list = find_matching_waypoint_list(aigp->target_name);
+		if ( aigp->wp_list_index < 0 ) {
+			aigp->wp_list_index = find_matching_waypoint_list_index(aigp->target_name);
 
-			if ( aigp->wp_list == NULL ) {
+			if ( aigp->wp_list_index < 0 ) {
 				Warning(LOCATION, "Unknown waypoint list %s - not found in mission file.  Killing ai goal", aigp->target_name );
 				return ai_achievability::NOT_ACHIEVABLE;
 			}
@@ -2344,7 +2344,7 @@ void ai_process_mission_orders( int objnum, ai_info *aip )
 			flags |= WPF_REPEAT;
 		if (current_goal->flags[AI::Goal_Flags::Waypoints_in_reverse])
 			flags |= WPF_BACKTRACK;
-		ai_start_waypoints(objp, current_goal->wp_list, flags, current_goal->int_data);
+		ai_start_waypoints(objp, current_goal->wp_list_index, flags, current_goal->int_data);
 		break;
 	}
 
diff --git a/code/ai/aigoals.h b/code/ai/aigoals.h
index 79868e0135c..9d8cd5475f3 100644
--- a/code/ai/aigoals.h
+++ b/code/ai/aigoals.h
@@ -119,7 +119,7 @@ typedef struct ai_goal {
 
 	const char *target_name;	// name of the thing that this goal acts upon
 	int		target_name_index;	// index of goal_target_name in Goal_target_names[][]
-	waypoint_list *wp_list;		// waypoints that this ship might fly.
+	int wp_list_index;			// waypoints that this ship might fly.
 	int target_instance;		// instance of thing this ship might be chasing (currently only used for weapons; note, not the same as objnum!)
 	int	target_signature;		// signature of object this ship might be chasing (currently only used for weapons; paired with above value to confirm target)
 
diff --git a/code/autopilot/autopilot.cpp b/code/autopilot/autopilot.cpp
index 42399eaaac8..9d89a629142 100644
--- a/code/autopilot/autopilot.cpp
+++ b/code/autopilot/autopilot.cpp
@@ -66,7 +66,7 @@ int start_dist;
 void autopilot_ai_waypoint_goal_fixup(ai_goal* aigp)
 {
 	// this function sets wp_index properly;
-	aigp->wp_list = find_matching_waypoint_list(aigp->target_name);
+	aigp->wp_list_index = find_matching_waypoint_list_index(aigp->target_name);
 }
 
 
@@ -111,13 +111,16 @@ const vec3d *NavPoint::GetPosition()
 {
 	if (flags & NP_WAYPOINT)
 	{
-		waypoint *wpt = find_waypoint_at_index((waypoint_list*) target_obj, waypoint_num-1);
-		Assert(wpt != NULL);
+		auto wp_list = find_waypoint_list_at_index(target_index);
+		auto wpt = find_waypoint_at_index(wp_list, waypoint_num-1);
+		Assert(wpt != nullptr);
+		if (wpt == nullptr)
+			return &vmd_zero_vector;
 		return wpt->get_pos();
 	}
 	else
 	{
-		return &Objects[((ship*) target_obj)->objnum].pos;
+		return &Objects[target_index].pos;
 	}
 }
 
@@ -462,12 +465,12 @@ bool StartAutopilot()
 			{ 
 				if (Navs[CurrentNav].flags & NP_WAYPOINT)
 				{
-					ai_add_ship_goal_player( AIG_TYPE_PLAYER_SHIP, AI_GOAL_WAYPOINTS_ONCE, 0, ((waypoint_list*)Navs[CurrentNav].target_obj)->get_name(), &Ai_info[Ships[i].ai_index] );
+					ai_add_ship_goal_player( AIG_TYPE_PLAYER_SHIP, AI_GOAL_WAYPOINTS_ONCE, 0, Waypoint_lists[Navs[CurrentNav].target_index].get_name(), &Ai_info[Ships[i].ai_index] );
 					//fixup has to wait until after wing goals
 				}
 				else
 				{
-					ai_add_ship_goal_player( AIG_TYPE_PLAYER_SHIP, AI_GOAL_FLY_TO_SHIP, 0, ((ship*)Navs[CurrentNav].target_obj)->ship_name, &Ai_info[Ships[i].ai_index] );
+					ai_add_ship_goal_player( AIG_TYPE_PLAYER_SHIP, AI_GOAL_FLY_TO_SHIP, 0, Ships[Objects[Navs[CurrentNav].target_index].instance].ship_name, &Ai_info[Ships[i].ai_index] );
 				}
 
 			}
@@ -491,7 +494,7 @@ bool StartAutopilot()
 				if (Navs[CurrentNav].flags & NP_WAYPOINT)
 				{
 					
-					ai_add_wing_goal_player( AIG_TYPE_PLAYER_WING, AI_GOAL_WAYPOINTS_ONCE, 0, ((waypoint_list*)Navs[CurrentNav].target_obj)->get_name(), i );
+					ai_add_wing_goal_player( AIG_TYPE_PLAYER_WING, AI_GOAL_WAYPOINTS_ONCE, 0, Waypoint_lists[Navs[CurrentNav].target_index].get_name(), i );
 
 					// "fix up" the goal
 					for (j = 0; j < MAX_AI_GOALS; j++)
@@ -505,7 +508,7 @@ bool StartAutopilot()
 				}
 				else
 				{
-					ai_add_wing_goal_player( AIG_TYPE_PLAYER_WING, AI_GOAL_FLY_TO_SHIP, 0, ((ship*)Navs[CurrentNav].target_obj)->ship_name, i );
+					ai_add_wing_goal_player( AIG_TYPE_PLAYER_WING, AI_GOAL_FLY_TO_SHIP, 0, Ships[Objects[Navs[CurrentNav].target_index].instance].ship_name, i );
 
 				}
 			}
@@ -874,12 +877,12 @@ void EndAutoPilot()
 	if (Navs[CurrentNav].flags & NP_WAYPOINT)
 	{
 		goal = AI_GOAL_WAYPOINTS_ONCE;
-		goal_name = ((waypoint_list*)Navs[CurrentNav].target_obj)->get_name();
+		goal_name = Waypoint_lists[Navs[CurrentNav].target_index].get_name();
 	}
 	else
 	{
 		goal = AI_GOAL_FLY_TO_SHIP;
-		goal_name = ((ship*)Navs[CurrentNav].target_obj)->ship_name;
+		goal_name = Ships[Objects[Navs[CurrentNav].target_index].instance].ship_name;
 	}
 
 	// assign ship goals
@@ -1094,9 +1097,9 @@ void NavSystem_Do()
 
 		for (i = 0; i < MAX_NAVPOINTS; i++)
 		{
-			if ((Navs[i].flags & NP_SHIP) && (Navs[i].target_obj != NULL))
+			if ((Navs[i].flags & NP_SHIP) && (Navs[i].target_index >= 0))
 			{
-				if (((ship*)Navs[i].target_obj)->objnum == -1)
+				if (Objects[Navs[i].target_index].flags[Object::Object_Flags::Should_be_dead])
 				{
 					if (CurrentNav == i)
 						CurrentNav = -1;
@@ -1108,7 +1111,7 @@ void NavSystem_Do()
 		// check if we're reached a Node
 		for (i = 0; i < MAX_NAVPOINTS; i++)
 		{
-			if (Navs[i].target_obj != NULL)
+			if (Navs[i].target_index >= 0)
 			{
 				if (Navs[i].flags & NP_VALIDTYPE && DistanceTo(i) < 1000)
 					Navs[i].flags |= NP_VISITED;
@@ -1392,7 +1395,7 @@ bool AddNav_Ship(const char *Nav, const char *TargetName, int flags)
 	{
 		if (Ships[i].objnum != -1 && !stricmp(TargetName, Ships[i].ship_name))
 		{
-			tnav.target_obj = (void *)&Ships[i];		
+			tnav.target_index = Ships[i].objnum;
 		}
 	}
 
@@ -1433,7 +1436,7 @@ bool AddNav_Waypoint(const char *Nav, const char *WP_Path, int node, int flags)
 
 	Assert(!(tnav.flags & NP_SHIP));
 
-	tnav.target_obj = find_matching_waypoint_list(WP_Path);
+	tnav.target_index = find_matching_waypoint_list_index(WP_Path);
 	tnav.waypoint_num = node;
 
 	// copy it into it's location
diff --git a/code/autopilot/autopilot.h b/code/autopilot/autopilot.h
index 9695ade8b1b..86646b88b41 100644
--- a/code/autopilot/autopilot.h
+++ b/code/autopilot/autopilot.h
@@ -34,7 +34,7 @@ class NavPoint
 	ubyte normal_color[3] = { 0x80, 0x80, 0xFF };
 	ubyte visited_color[3] = { 0xFF, 0xFF, 0x00 };
 
-	const void *target_obj = nullptr;
+	int target_index = -1; //waypoint list index if NP_WAYPOINT, otherwise object index
 	int waypoint_num = -1; //only used when flags & NP_WAYPOINT
 
 	const vec3d *GetPosition();
@@ -53,7 +53,7 @@ class NavPoint
 		visited_color[1] = 0xFF;
 		visited_color[2] = 0x00;
 
-		target_obj = nullptr;
+		target_index = -1;
 		waypoint_num = -1;
 	}
 };
diff --git a/code/mission/missiontraining.cpp b/code/mission/missiontraining.cpp
index 036f219ccb4..8b68c91d44f 100644
--- a/code/mission/missiontraining.cpp
+++ b/code/mission/missiontraining.cpp
@@ -92,7 +92,7 @@ int	Training_context_speed_set;
 int	Training_context_speed_min;
 int	Training_context_speed_max;
 TIMESTAMP	Training_context_speed_timestamp;
-waypoint_list *Training_context_path;
+int Training_context_waypoint_path;
 int Training_context_goal_waypoint;
 int Training_context_at_waypoint;
 float	Training_context_distance;
@@ -398,7 +398,7 @@ void training_mission_init()
 	Training_context = 0;
 	Training_context_speed_set = 0;
 	Training_context_speed_timestamp = TIMESTAMP::invalid();
-	Training_context_path = nullptr;
+	Training_context_waypoint_path = -1;
 
 	Players_target = UNINITIALIZED;
 	Players_mlocked = UNINITIALIZED;
diff --git a/code/mission/missiontraining.h b/code/mission/missiontraining.h
index f039b6b959f..4e3a298043f 100644
--- a/code/mission/missiontraining.h
+++ b/code/mission/missiontraining.h
@@ -25,7 +25,7 @@ extern int Training_context_speed_min;
 extern int Training_context_speed_max;
 extern int Training_context_speed_set;
 extern TIMESTAMP Training_context_speed_timestamp;
-extern waypoint_list *Training_context_path;
+extern int Training_context_waypoint_path;
 extern int Training_context_goal_waypoint;
 extern int Training_context_at_waypoint;
 extern float Training_context_distance;
diff --git a/code/network/multi_obj.cpp b/code/network/multi_obj.cpp
index b842e2e8105..3902f495a4e 100644
--- a/code/network/multi_obj.cpp
+++ b/code/network/multi_obj.cpp
@@ -1493,8 +1493,10 @@ int multi_oo_pack_data(net_player *pl, object *objp, ushort oo_flags, ubyte *dat
 		// either send out the waypoint they are trying to get to *or* their current target
 		if (umode == AIM_WAYPOINTS) {
 			// if it's already started pointing to a waypoint, grab its net_signature and send that instead
-			if ((aip->wp_list != nullptr) && (aip->wp_index >= 0 && aip->wp_index < static_cast<int>(aip->wp_list->get_waypoints().size()))) {
-				target_signature = Objects[aip->wp_list->get_waypoints().at(aip->wp_index).get_objnum()].net_signature;
+			waypoint_list* wpl;
+			waypoint* wp;
+			if (((wpl = find_waypoint_list_at_index(aip->wp_list_index)) != nullptr) && ((wp = find_waypoint_at_index(wpl, aip->wp_index)) != nullptr)) {
+				target_signature = Objects[wp->get_objnum()].net_signature;
 			}
 		} // send the target signature. 2021 Version!
 		else if ((aip->goals[0].target_name != nullptr) && strlen(aip->goals[0].target_name) != 0) {
@@ -2124,12 +2126,15 @@ int multi_oo_unpack_data(net_player* pl, ubyte* data, int seq_num, int time_delt
 					Ai_info[shipp->ai_index].goals[0].target_name = nullptr;
 				// set their waypoints if in waypoint mode.
 				} else if (umode == AIM_WAYPOINTS) {
-					waypoint* destination = find_waypoint_with_instance(target_objp->instance);
-					if (destination != nullptr) {
-						Ai_info[shipp->ai_index].wp_list = destination->get_parent_list();
-						Ai_info[shipp->ai_index].wp_index = find_index_of_waypoint(Ai_info[shipp->ai_index].wp_list, destination);
+					int wp_list_index = calc_waypoint_list_index(target_objp->instance);
+					int wp_index = calc_waypoint_index(target_objp->instance);
+					waypoint_list* wpl;
+					if (((wpl = find_waypoint_list_at_index(wp_list_index)) != nullptr) && (find_waypoint_at_index(wpl, wp_index) != nullptr)) {
+						Ai_info[shipp->ai_index].wp_list_index = wp_list_index;
+						Ai_info[shipp->ai_index].wp_index = wp_index;
 					} else {
-						Ai_info[shipp->ai_index].wp_list = nullptr;
+						Ai_info[shipp->ai_index].wp_list_index = -1;
+						Ai_info[shipp->ai_index].wp_index = INVALID_WAYPOINT_POSITION;
 					}
 				} else {
 					Ai_info[shipp->ai_index].target_objnum = OBJ_INDEX(target_objp);
diff --git a/code/object/waypoint.cpp b/code/object/waypoint.cpp
index f02f1fcc370..4c5940430f9 100644
--- a/code/object/waypoint.cpp
+++ b/code/object/waypoint.cpp
@@ -198,7 +198,7 @@ void waypoint_create_game_objects()
 
 waypoint_list *find_matching_waypoint_list(const char *name)
 {
-	Assert(name != NULL);
+	Assert(name != nullptr);
 
 	for (auto &ii: Waypoint_lists)
 	{
@@ -206,7 +206,22 @@ waypoint_list *find_matching_waypoint_list(const char *name)
 			return &ii;
 	}
 
-	return NULL;
+	return nullptr;
+}
+
+int find_matching_waypoint_list_index(const char *name)
+{
+	Assert(name != nullptr);
+
+	int i = 0;
+	for (auto &ii: Waypoint_lists)
+	{
+		if (!stricmp(ii.get_name(), name))
+			return i;
+		i++;
+	}
+
+	return -1;
 }
 
 // NOTE: waypoint names are always in the format Name:index
@@ -320,23 +335,18 @@ waypoint *find_waypoint_with_instance(int waypoint_instance)
 
 waypoint_list *find_waypoint_list_at_index(int index)
 {
-	Assert(index >= 0);
-
-	if (index >= 0 && index < (int)Waypoint_lists.size())
+	if (SCP_vector_inbounds(Waypoint_lists, index))
 		return &Waypoint_lists[index];
 
-	return NULL;
+	return nullptr;
 }
 
 waypoint *find_waypoint_at_index(waypoint_list *list, int index)
 {
-	Assert(list != NULL);
-	Assert(index >= 0);
-
-	if (index >= 0 && index < (int)list->get_waypoints().size())
+	if (list && SCP_vector_inbounds(list->get_waypoints(), index))
 		return &list->get_waypoints()[index];
 
-	return NULL;
+	return nullptr;
 }
 
 int find_index_of_waypoint_list(const waypoint_list *wp_list)
@@ -417,7 +427,7 @@ int waypoint_add(const vec3d *pos, int waypoint_instance)
 	{
 		// get a name for it
 		char buf[NAME_LENGTH];
-		waypoint_find_unique_name(buf, (int)(Waypoint_lists.size() + 1));
+		waypoint_find_unique_name(buf, static_cast<int>(Waypoint_lists.size()) + 1);
 
 		// add new list with that name
 		waypoint_list new_list(buf);
@@ -425,8 +435,8 @@ int waypoint_add(const vec3d *pos, int waypoint_instance)
 		wp_list = &Waypoint_lists.back();
 
 		// set up references
-		wp_list_index = (int)(Waypoint_lists.size() - 1);
-		wp_index = (int) wp_list->get_waypoints().size();
+		wp_list_index = static_cast<int>(Waypoint_lists.size()) - 1;
+		wp_index = static_cast<int>(wp_list->get_waypoints().size());
 	}
 	// create the waypoint on the same list as, and immediately after, waypoint_instance
 	else
@@ -439,7 +449,7 @@ int waypoint_add(const vec3d *pos, int waypoint_instance)
 
 		// it has to be on, or at the end of, an existing list
 		Assert(wp_list != NULL);
-		Assert((uint) wp_index <= wp_list->get_waypoints().size());
+		Assert(wp_index <= static_cast<int>(wp_list->get_waypoints().size()));
 
 		// iterate through all waypoints that are at this index or later,
 		// and edit their instances so that they point to a waypoint one place higher
diff --git a/code/object/waypoint.h b/code/object/waypoint.h
index f59332b6bfa..06cb04862bb 100644
--- a/code/object/waypoint.h
+++ b/code/object/waypoint.h
@@ -72,6 +72,7 @@ void waypoint_create_game_objects();
 
 // Find a waypoint list with the specified name
 waypoint_list *find_matching_waypoint_list(const char *name);
+int find_matching_waypoint_list_index(const char *name);
 
 // Find a waypoint with the specified name (e.g. Path:1)
 waypoint *find_matching_waypoint(const char *name);
diff --git a/code/parse/sexp.cpp b/code/parse/sexp.cpp
index 5644a779f8c..084adf976ab 100644
--- a/code/parse/sexp.cpp
+++ b/code/parse/sexp.cpp
@@ -20215,7 +20215,8 @@ int sexp_waypoint_twice()
 int sexp_path_flown()
 {
 	if (Training_context & TRAINING_CONTEXT_FLY_PATH) {
-		if ((uint) Training_context_goal_waypoint == Training_context_path->get_waypoints().size()){
+		auto wp_list = find_waypoint_list_at_index(Training_context_waypoint_path);
+		if (wp_list && (Training_context_goal_waypoint == static_cast<int>(wp_list->get_waypoints().size()))) {
 			return SEXP_TRUE;
 		}
 	}
@@ -24990,8 +24991,8 @@ void sexp_set_training_context_fly_path(int node)
 		return;
 
 	Training_context |= TRAINING_CONTEXT_FLY_PATH;
-	Training_context_path = wp_list;
-	Training_context_distance = (float)distance;
+	Training_context_waypoint_path = find_index_of_waypoint_list(wp_list);
+	Training_context_distance = static_cast<float>(distance);
 	Training_context_goal_waypoint = 0;
 	Training_context_at_waypoint = -1;
 }
diff --git a/code/scripting/api/libs/mission.cpp b/code/scripting/api/libs/mission.cpp
index 7273f1626c6..0b00d52fbb4 100644
--- a/code/scripting/api/libs/mission.cpp
+++ b/code/scripting/api/libs/mission.cpp
@@ -1269,8 +1269,8 @@ ADE_FUNC(createWaypoint, l_Mission, "[vector Position, waypointlist List]",
 	int waypoint_instance = -1;
 	if (wlh && wlh->isValid())
 	{
-		int wp_list_index = find_index_of_waypoint_list(wlh->wlp);
-		int wp_index = (int) wlh->wlp->get_waypoints().size() - 1;
+		int wp_list_index = find_index_of_waypoint_list(wlh->getList());
+		int wp_index = static_cast<int>(wlh->getList()->get_waypoints().size()) - 1;
 		waypoint_instance = calc_waypoint_instance(wp_list_index, wp_index);
 	}
 	int obj_idx = waypoint_add(v3 != NULL ? v3 : &vmd_zero_vector, waypoint_instance);
diff --git a/code/scripting/api/objs/order.cpp b/code/scripting/api/objs/order.cpp
index 3c2017aeebc..df78c346850 100644
--- a/code/scripting/api/objs/order.cpp
+++ b/code/scripting/api/objs/order.cpp
@@ -243,7 +243,7 @@ ADE_VIRTVAR(Target, l_Order, "object", "Target of the order. Value may also be a
 									flags |= WPF_REPEAT;
 								if (ohp->aigp->flags[AI::Goal_Flags::Waypoints_in_reverse])
 									flags |= WPF_BACKTRACK;
-								ai_start_waypoints(ohp->objh.objp(), wpl, flags, ohp->aigp->int_data);
+								ai_start_waypoints(ohp->objh.objp(), find_index_of_waypoint_list(wpl), flags, ohp->aigp->int_data);
 							}
 						}
 					}
@@ -303,9 +303,9 @@ ADE_VIRTVAR(Target, l_Order, "object", "Target of the order. Value may also be a
 		case AI_GOAL_WAYPOINTS:
 		case AI_GOAL_WAYPOINTS_ONCE:
 			// check if waypoint order is the current goal (ohp->odx == 0) and if it is valid
-			if ( (ohp->odx == 0) && (aip->wp_index != INVALID_WAYPOINT_POSITION) &&
-				(aip->wp_index >= 0 && aip->wp_index < static_cast<int>(aip->wp_list->get_waypoints().size())) ) {
-				objnum = aip->wp_list->get_waypoints()[aip->wp_index].get_objnum();
+			waypoint* wp;
+			if ( (ohp->odx == 0) && (aip->wp_index != INVALID_WAYPOINT_POSITION) && ((wpl = find_waypoint_list_at_index(aip->wp_list_index)) != nullptr) && ((wp = find_waypoint_at_index(wpl, aip->wp_index)) != nullptr) ) {
+				objnum = wp->get_objnum();
 			} else {
 				wpl = find_matching_waypoint_list(ohp->aigp->target_name);
 				if (wpl != nullptr) {
diff --git a/code/scripting/api/objs/waypoint.cpp b/code/scripting/api/objs/waypoint.cpp
index 49bd22cca31..652c59ea679 100644
--- a/code/scripting/api/objs/waypoint.cpp
+++ b/code/scripting/api/objs/waypoint.cpp
@@ -31,25 +31,38 @@ ADE_FUNC(getList, l_Waypoint, NULL, "Returns the waypoint list", "waypointlist",
 	return ade_set_error(L, "o", l_WaypointList.Set(waypointlist_h()));
 }
 
-waypointlist_h::waypointlist_h() {wlp=NULL;name[0]='\0';}
-waypointlist_h::waypointlist_h(waypoint_list* n_wlp) {
-	wlp = n_wlp;
-	if(n_wlp != NULL) {
+waypointlist_h::waypointlist_h()
+	: wl_index(-1)
+{
+	name[0] = '\0';
+}
+waypointlist_h::waypointlist_h(int _wl_index)
+{
+	if (SCP_vector_inbounds(Waypoint_lists, _wl_index))
+	{
+		wl_index = _wl_index;
+		auto wlp = &Waypoint_lists[wl_index];
 		strcpy_s(name, wlp->get_name());
-	} else {
-		memset(name, 0, sizeof(name));
+	}
+	else
+	{
+		wl_index = -1;
+		name[0] = '\0';
 	}
 }
+waypointlist_h::waypointlist_h(waypoint_list* _wlp)
+	: waypointlist_h((_wlp == nullptr) ? -1 : static_cast<int>(_wlp - Waypoint_lists.data()))
+{}
 waypointlist_h::waypointlist_h(const char* wlname)
+	: waypointlist_h((wlname == nullptr) ? nullptr : find_matching_waypoint_list(name))
+{}
+bool waypointlist_h::isValid() const
 {
-	wlp = NULL;
-	if ( wlname != NULL ) {
-		strcpy_s(name, wlname);
-		wlp = find_matching_waypoint_list(wlname);
-	}
+	return SCP_vector_inbounds(Waypoint_lists, wl_index);
 }
-bool waypointlist_h::isValid() const {
-	return (wlp != NULL && !strcmp(wlp->get_name(), name));
+waypoint_list* waypointlist_h::getList() const
+{
+	return isValid() ? &Waypoint_lists[wl_index] : nullptr;
 }
 
 //**********HANDLE: WaypointList
@@ -58,8 +71,7 @@ ADE_OBJ(l_WaypointList, waypointlist_h, "waypointlist", "waypointlist handle");
 ADE_INDEXER(l_WaypointList, "number Index", "Array of waypoints that are part of the waypoint list", "waypoint", "Waypoint, or invalid handle if the index or waypointlist handle is invalid")
 {
 	int idx = -1;
-	waypointlist_h* wlh = NULL;
-	char wpname[128];
+	waypointlist_h* wlh = nullptr;
 	if( !ade_get_args(L, "oi", l_WaypointList.GetPtr( &wlh ), &idx))
 		return ade_set_error( L, "o", l_Waypoint.Set( object_h() ) );
 
@@ -69,12 +81,10 @@ ADE_INDEXER(l_WaypointList, "number Index", "Array of waypoints that are part of
 	//Lua-->FS2
 	idx--;
 
-	//Get waypoint name
-	sprintf(wpname, "%s:%d", wlh->wlp->get_name(), calc_waypoint_index(idx) + 1);
-	waypoint *wpt = find_matching_waypoint( wpname );
-	if( (idx >= 0) && ((uint) idx < wlh->wlp->get_waypoints().size()) && (wpt != NULL) && (wpt->get_objnum() >= 0) ) {
-		return ade_set_args(L, "o", l_Waypoint.Set(object_h(&Objects[wpt->get_objnum()])));
-	}
+	//Get waypoint
+	auto wp = find_waypoint_at_index(wlh->getList(), idx);
+	if (wp)
+		return ade_set_args(L, "o", l_Waypoint.Set(object_h(wp->get_objnum())));
 
 	return ade_set_error(L, "o", l_Waypoint.Set( object_h() ) );
 }
@@ -86,11 +96,11 @@ ADE_FUNC(__len, l_WaypointList,
 		 "number",
 		 "Number of waypoints in the list, or 0 if handle is invalid")
 {
-	waypointlist_h* wlh = NULL;
+	waypointlist_h* wlh = nullptr;
 	if ( !ade_get_args(L, "o", l_WaypointList.GetPtr(&wlh)) ) {
 		return ade_set_error( L, "o", l_Waypoint.Set( object_h() ) );
 	}
-	return ade_set_args(L, "i", wlh->wlp->get_waypoints().size());
+	return ade_set_args(L, "i", wlh->getList()->get_waypoints().size());
 }
 
 ADE_VIRTVAR(Name, l_WaypointList, "string", "Name of WaypointList", "string", "Waypointlist name, or empty string if handle is invalid")
@@ -102,7 +112,7 @@ ADE_VIRTVAR(Name, l_WaypointList, "string", "Name of WaypointList", "string", "W
 	}
 
 	if(ADE_SETTING_VAR && s != NULL) {
-		wlh->wlp->set_name(s);
+		wlh->getList()->set_name(s);
 		strcpy_s(wlh->name,s);
 	}
 
diff --git a/code/scripting/api/objs/waypoint.h b/code/scripting/api/objs/waypoint.h
index b05cdae4b1b..e03a4e5f9aa 100644
--- a/code/scripting/api/objs/waypoint.h
+++ b/code/scripting/api/objs/waypoint.h
@@ -12,12 +12,14 @@ DECLARE_ADE_OBJ(l_Waypoint, object_h);
 
 struct waypointlist_h
 {
-	waypoint_list *wlp;
+	int wl_index;
 	char name[NAME_LENGTH];
 	waypointlist_h();
-	explicit waypointlist_h(waypoint_list *n_wlp);
+	explicit waypointlist_h(int _wl_index);
+	explicit waypointlist_h(waypoint_list* _wlp);
 	explicit waypointlist_h(const char* wlname);
 	bool isValid() const;
+	waypoint_list* getList() const;
 };
 
 DECLARE_ADE_OBJ(l_WaypointList, waypointlist_h);
diff --git a/code/ship/ship.cpp b/code/ship/ship.cpp
index 1bda9545226..fe89d92a40e 100644
--- a/code/ship/ship.cpp
+++ b/code/ship/ship.cpp
@@ -17140,9 +17140,10 @@ int ship_return_seconds_to_goal(ship *sp)
 	if ( aip->mode == AIM_WAYPOINTS ) {
 		// Is traveling a waypoint path
 		min_speed = 0.9f * max_speed;
-		if (aip->wp_list != NULL) {
+		auto wp_list = find_waypoint_list_at_index(aip->wp_list_index);
+		if (wp_list != nullptr) {
 			Assert(aip->wp_index != INVALID_WAYPOINT_POSITION);
-			auto& waypoints = aip->wp_list->get_waypoints();
+			auto& waypoints = wp_list->get_waypoints();
 
 			// distance to current waypoint
 			dist += vm_vec_dist_quick(&objp->pos, waypoints[aip->wp_index].get_pos());
diff --git a/freespace2/freespace.cpp b/freespace2/freespace.cpp
index 3ed6035a101..cd35a6bd2de 100644
--- a/freespace2/freespace.cpp
+++ b/freespace2/freespace.cpp
@@ -7042,7 +7042,7 @@ void game_do_training_checks()
 	}
 
 	if (Training_context & TRAINING_CONTEXT_FLY_PATH) {
-		wplp = Training_context_path;
+		wplp = find_waypoint_list_at_index(Training_context_waypoint_path);
 		if (wplp->get_waypoints().size() > (uint) Training_context_goal_waypoint) {
 			i = Training_context_goal_waypoint;
 			do {