THIS IS A SPOILER PAGE.
YOU HAVE BEEN WARNED.
The purpose of this page is to provide approximate locations for every secondary objective within the game, along with the author's view on whether or not they should be avoided or collected. No matter how hard they are to reach they all reward 5XP each.
2) Deck 14 Alta Sector - 1x SO. Crates in SW corner of map, through the tunnels behind Xeno spawn area. Provides 100SP. Useful for summoning higher level Engineers on new game+, less essential on first play through.
3) Deck 14 Power Relay Grid - 1X SO. Crates just west of the centre of the map, near a switch. Very easy to grab.
5) Alien Vessel: Bomb Escort - 2X SO. Enemy held tact points (TP). One is in southwest corner of map, the other is on the eastern side of the map. Generally avoid, as it is quicker & safer to deliver the payload as a unit.
2) Siege at Tundeer - 5x SO. Crates to the west of the eastern gate. 2 items in a bunker in the centre of the map (only needs 1 templar). Fuel drums in bunker halfway between the eastern gate and the southern TP. In a small room to the southeast of the bunker containing southern gate mechanism. All 5 are fairly straightforward to collect.
4) Extermination By Fire - 2x SO. Crates south of northern tact point (or to the immediate NE of the red square a Soldier will advise taking Overwatch from). Computer panel to north of northern xeno spore fragment (and west of the Northern Xeno-controlled TP). Grab the one near the TP, ignore the other unless you've got a Scout or your Cap specced with MP talents.
1) Patrol Route - 2x SO. In buildings very near deployment area, one to the south-south east, the other to the northwest. Can grab both by end of turn 2.
1.1) (optional) Kaldun: Factory Entrance - 2X SO. Northern edge of the map just after the trench section. Southern edge of map in the trenches (dark brown ground). Both are straightforward to collect.
1.2) (optional) Kaldun: Factory Core - 6X SO. East of central TP (health packs); Northern end and southern end of room with western TP; both are on the western side of the room. 1 in north east corner of map; to the far north of eastern TP. 1 in SE corner of map to the far south of Eastern TP. 1 on southern edge in a small room between the southern deployment zone and southeast corner. Don't attempt to collect all SO unless you plan to go over turn limit. For the easiest collection run start in the southern deployment zone, go east to grab the 2 there, ignore northeast corner, take medikits in the centre and aim for one in the western room.
2) Trench Warfare - 2x SO. Computer panel to north-northwest of deployment area. Bunker entrance to north of trench between 1st and 2nd computer panel. 2 templar team can grab both; solo templar not advised unless it's just the bunker you're after (lots of soldiers).
3) Drayan Core - 4x SO. 2 are highlighted as part of the mission - look for bunkers near the AA guns. 1 is in the second large bunker, which is north of complex gate a.k.a. exit (fuel drums - hydra ordnance). 1 is in a small bunker to the north east of the second large bunker. Depends on difficulty as to whether to go for all four or just a few.
5) Extermination Protocol - 2x SO. Crates to the far north of eastern tower, in a dead end(par with central tower). Fuel drums to the north-north east of central tower. Ignore both as they take too long to collect safely given the re-spawning Litch and the need to defend your TP.
1a/2b) Airlock Chambers - 2X SO. Northwest of 1st open door button. Southeast of 2nd close door button. In both cases you must travel down a long corridor before you reach the objective. You'll get better returns going for a speed run.
1b/2a) Boarding - 6X SO. All 6 are red fuel drums. Templar who deploys in SE corner can grab one en route to Engineer at southern TP. Captain & Scout head in opposite directions; one goes to south to reach Engineer and collects en-route, the other heads north-northeast to collect. Templar at north of map heads east-northeast to collect one, then heads south-southeast over stairs to collect another. The last one is next to the enemy held TP in the northeast corner. Getting 5 should be considered par.
3) Power Relay - 3X SO. 1st: Generator to the immediate east of deployment area (easily missed) in the blue tiles (the ones that are powering the relay objective switches). Non-Engineers can complete this objective. 2nd: Crates to southeast of 4th switch in chain (middle of second row). If this is confusing you, it's also to the immediate NE of the first relay switch you activate. 3rd: Crates to the west of 5th switch in chain (middle of third row). All 3 are easy grabs.
4a) Atmo Reentry - 1X SO. Computer panel on the east side of map, half way between start point and eastern extraction point. Keep heading south and east to of the TP you find. Straightforward to grab, just don't split team up too much as you've got 4 escorts to protect.
4b) Cargo: Atmo Reentry - 3X SO. Crates with 2x Reactor Jolts northeast of the TP just north of the starting area. Crates in the southernmost corridor with 2 Minor Medikits. 3rd SO location unknown.
1) Infiltration Site - 1X SO. Is northwest of the first TP you must capture.
2) Drop Shaft - 1X SO. Is a group of crates on west of map, parallel with the TP. You must go between two major spawn areas to collect; safer to ignore.
3) Tunnel Complex - 3X SO. East of eastern TP. Northwest corner of map (northwest of northern TP). North east corner of map. Can complete with 15-20% speed bonus by ditching SO, as every templar must reach evacuation point to finish mission.
4) Artifact Vaults - 1X SO. Collect all 4 artifacts. Artifacts are Southwest, Northwest, North-Northwest and Northeast of deployment area. Northeast is the area where I've encountered the most danger; North-Northwest is safest.
5) Detonation Site - 2X SO. Crates that are in the Southwest and Southeast corners of the map. It is an asymmetric map as Southwest corner sits higher than Southeast corner by about 8 tiles. In both cases, you have to go past a detonation site by 7-10 tiles to reach a SO. Not worth collecting due to time spent waiting for the engineer to arrive and the level of risk involved (you're entering a Terrox nest).
1) Dread Falcon - 3X SO. Crates en route to southwest primary objective. Crates to the west of the central primary objective. Loading bay to east of central primary objective. All three are easy to collect. If you want a speed bonus as well, send a templar to the North and have them touch the extraction point once all primary objectives have been collected.
2) Leo Dropzone - 3X SO. The TP counts as a secondary in this mission plus the two sets of near by crates (southwest & north of TP). Use TP as your last stand location.
3) Southbound Trail - 2X SO. Barracks entrance (soldier spawn point) on west side of the map after moving south a third of the way to the end point. Computer relay on the east side of the map about half way between start and end point. This is a long, narrow map so collecting at least one of the two is achievable. Bring a scout to plot your path.
4) Traitor's Bunker - 2X SO. Crates to northwest of radio relay (in corridor, near pipes). Crates to southeast of radio relay.
1) Drop Zone - 3X SO, 3X ESCORT (hidden). 2 are xeno pods which require a hydra to flame. One pods is north of the deployment area, the other is east of the deployment area. Third is supply crates to east of eastern xeno pod. Best pattern is to go north with squad to secure TP, then send hydra Southeast to flame the other xeno pod and finally east to visit crates and then rescue the civilians.
The 3 unarmed survivors are located at the eastern map edge in a large building, not far from the south east corner. Alternatively head south from the eastern TP. Only rescue them once the mission is going to end (i.e you can capture your third TP). The room has 2 sets working doors (southwest and north) and a destroyed door (southeast) with adjacent spawn point. Spawn point is within 8 tiles of the survivors.
2) Starport Breach - 2X SO. Both are in a room to the east-northeast of 2nd TP. Head Northeast past barracks entrance to a medium sized sealed room with 2 sets of crates, one is further away than the other. The second door on the northern edge of the room takes you southeast of the final TP you must capture. Worth going for, as it prevents being surrounded going via the route the mission shows you. Don't expect all the soldiers you start with to survive; you're more likely to finish with 2 of the 5.
3) Orbital Defence Battery 2X SO. A set of crates in a bunker that is northeast of the western TP/west of the northern TP (the crates provide 400SP so are a definite must). In the building to the northeast of the of deployment area (non-urgent collection). There isn't anywhere truly safe to put the 3 soldiers.
4) Starport Vault - 3X SO. All are crates: northwest of war worms initial deployment; Northeast of initial TP, near worm hole on east side of map; Northwest of second TP in northeast corner of map. Due to the random nature of the mission, only collect if your squad needs to head in that direction.
Stratos Space Station (Epilogue)
1) Central Airlock - 3X SO. Crates to north of eastern TP/southeast of Northern TP. Crates to south east of southern gate. Crates to southwest of southern gate. The map is circular, so you can move out from the centre to a TP and go around in a loop. Only the southern door of the central hub can't be secured. Best method is send a scout to collect the southern objectives, whilst the rest of the squad capture the western TP. Regroup to take the eastern TP and collect the final set of crates.
2) Defence Relay - 1X SO. Activate all 6 turret destruction switches. IGNORE. Take down as many turrets as needed to provide a clear path to the evacuation point. This map is not nice due to all the range 6 turrets.
3) Elevator Complex - 3X SO. Crates to north of switch on level 1 (easy grab). Activating both lift switches on east side of level 1 - northeast and south east corners; this doubles lift capacity, so is a must do. Crates to the southwest of the switch on level 2 (optional detour).
4a) Command Centre - 1X SO. To the northeast of the southern TP in a 3x3 room that is accessed by narrow corridors. There are multiple corridors that lead into this room.
4b) Research Hall - 5X SO. Head south down the middle bridge of the three bridges and enter the sealed room to find crates (assault overflow). In a sealed room directly east of previous SO (reactor jolt). In a sealed room to E-SE of lab where Mariale & 2 scientists (Escort) are holed up (Southeast corner of map with commander resupply). Crates (reactor jolt) in a sealed room on west side of the research complex (to the west of the western data room). Collecting data from both data rooms is supposed to become a secondary objective in the event that Mariale reaches the elevator. This doesn't happen as of build 2.7.5. You have to settle for 4 secondaries plus safely escorting 2 unarmed scientists.
5) Reactor Core - 2X SO. Crates (medikit) in the northwest corner of the map at a dead end near a spawn point; head west at the first square metal platform with defensive points to find. Crates (assault overflow & commander's resupply) to the southeast of southern TP, between the two bridges that lead to the eastern hostile turret. Turrets are deactivated if mission 4a is performed; 4b sees the turrets remain live. This mission has a very difficult turn limit unless you split your force in two, so collect the bonuses as you'll likely exceed the turn limit.