Use battle.hasThreats to determine if all enemies have been defeated.

src/battle/entities.c

@@ -67,7 +67,7 @@ void doEntities(void)
 
 	prev = &battle.entityHead;
 
-	numAllies = numEnemies = numActiveAllies = numActiveEnemies = numSpawnedEnemies = 0;
+	battle.hasThreats = numAllies = numEnemies = numActiveAllies = numActiveEnemies = numSpawnedEnemies = 0;
 
 	if (dev.playerImmortal)
 	{
@@ -218,6 +218,11 @@ void doEntities(void)
 						numSpawnedEnemies++;
 					}
 				}
+				
+				if (e->health > 0 && !(e->flags & EF_DISABLED))
+				{
+					battle.hasThreats = 1;
+				}
 			}
 		}
 

src/battle/objectives.c

@@ -120,7 +120,7 @@ void updateObjective(char *name, int type)
 					}
 				}
 				
-				if (o->isEliminateAll && o->status != OS_COMPLETE && (battle.stats[STAT_ENEMIES_KILLED] + battle.stats[STAT_CAPITAL_SHIPS_DESTROYED]) == battle.numInitialEnemies)
+				if (o->isEliminateAll && o->status != OS_COMPLETE && !battle.hasThreats)
 				{
 					addHudMessage(colors.green, _("%s - Objective Complete!"), o->description);
 					

src/battle/script.c

@@ -262,7 +262,7 @@ static void executeNextLine(ScriptRunner *runner)
 	}
 	else if (strcmp(command, "END_CHALLENGE") == 0)
 	{
-		game.currentMission->challengeData.scriptedEnd = 1;
+		battle.scriptedEnd = 1;
 	}
 	else if (strcmp(command, "RETREAT_ALLIES") == 0)
 	{

src/challenges/challenges.c

@@ -89,8 +89,6 @@ void loadChallenge(Mission *mission, cJSON *node)
 	int i;
 	Challenge *challenge;
 	
-	memset(&mission->challengeData, 0, sizeof(ChallengeData));
-	
 	mission->challengeData.isChallenge = 1;
 
 	/* limits */
@@ -117,6 +115,7 @@ void loadChallenge(Mission *mission, cJSON *node)
 	/* misc */
 	mission->challengeData.allowPlayerDeath = getJSONValue(node, "allowPlayerDeath", 0);
 	mission->challengeData.clearWaypointEnemies = getJSONValue(node, "clearWaypointEnemies", 0);
+	mission->challengeData.eliminateThreats = getJSONValue(node, "eliminateThreats", 0);
 
 	node = cJSON_GetObjectItem(node, "challenges");
 
@@ -208,7 +207,12 @@ static int challengeFinished(void)
 		return 1;
 	}
 	
-	return (player->health <= 0 || player->alive == ALIVE_ESCAPED || game.currentMission->challengeData.scriptedEnd);
+	if (game.currentMission->challengeData.eliminateThreats && !battle.hasThreats)
+	{
+		return 1;
+	}
+	
+	return (player->health <= 0 || player->alive == ALIVE_ESCAPED || battle.scriptedEnd);
 }
 
 static int updateChallenges(void)

src/structs.h

@@ -262,9 +262,9 @@ typedef struct {
 	int noBoost;
 	int noECM;
 	int noGuns;
-	int scriptedEnd;
 	int allowPlayerDeath;
 	int clearWaypointEnemies;
+	int eliminateThreats;
 	Challenge *challenges[MAX_CHALLENGES];
 } ChallengeData;
 
@@ -345,6 +345,8 @@ typedef struct {
 	int radarRange;
 	int numPlayerGuns;
 	int numObjectivesComplete, numObjectivesTotal, numConditions;
+	int scriptedEnd;
+	int hasThreats;
 	Entity *missionTarget;
 	Entity *jumpgate;
 	Entity *messageSpeaker;