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Path of Exile Fall of Oriath 3.0 Atlas Unlocking Guide (To be immediately obsolete in 3.1)
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TIP 1 : Remember to check the maps that Zana sells everytime she levels up and after every daily mission!
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TIP 2 : If you don't care about your T1 - T4 Shaper orbs, you can use them to shape maps that you can sell for missing maps in your Atlas
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Step 1 : Unlock all T1 maps
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Step 2 : Unlock Factory, Beach, and Oasis T2 maps before going to T3 maps. Try to make sure you have a Cavern, Marshes, and Grotto map (from Factory, Beach, and Oasis). Unlock Ghetto.
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Step 3 : Unlock Sewer, then move to unlocking the other T3 maps. Try to get get a Graveyard Map (can trade 3 Sewers into a Graveyard)
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Step 4 : Unlock Graveyard, then try to unlock Academy. After unlocking Academy, unlock Acid Lakes and Phantasmagoria. Try to find a Pit map in Acid Lakes and Primordial Pool map in Phantasmagoria before unlocking other T4 maps. If you get Pit map before Primordial Pool, you can unlock Waste Pool (T4 map) to have another map to run to find Primordial Pool maps. After Pit and Primordial Pool is unlocked, you can unlock the other T4 maps.
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Step 5 : Unlock Peninsula, then don't unlock any other map until you find Ramparts. You're trying to unlock Ramparts and Spider Lair in T5. Once both of those are unlocked, you can unlock rest of T5.
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Step 6 : Unlock Vaal City, then unlock Arachnid Tomb. Once you unlock Arachnid Tomb you can unlock the rest of T6. 
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Step 7 : Unlock Armoury, Cells, and Castle Ruins. Do not unlock any other T7 until you get a Bog, Barrows, and Arena map from Castle Ruins, Cells, and Armoury respectively. Once you find those you can unlock the rest of the T7 maps. If you find Bog and Arena before Barrows, you can unlock Bog.
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Step 7 : Unlock Armoury, Cells, and Castle Ruins. Do not unlock any other T7 until you get a Bog, Barrows, and Arena map from Castle Ruins, Cells, and Armoury respectively. Once you find those you can unlock the rest of the T7 maps. If you find Bog and Arena before Barrows, you can unlock Bog. Bog cannot result from the result of vendoring maps, so be sure to to acquire a Bog map.
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Step 8 : Unlock Tropical Island, do not unlock any other T8 until you find Reef. After getting Reef, unlock the rest of the T8s. If you unlocked Bog earlier to run a higher tier map in Step 7, you need to find Reef and Barrows before unlocking the rest of the T8s.
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Step 9 : Unlock Promenade first, try to run Promenades to find Museum and Colonnade (Colonnade for the T5 shaper orb, only need 1, then remove from Atlas). If you found Museum, you can unlock the rest of the T9s, but you only need Promenade and Temple maps. Temples maps you need 10 - 1 to unlock, then 9 to vendor for an excavation map (3 Temple -> 1 Malformation map, 3 Malformation map -> 1 Excavation map). Run Excavation to unlock the T6 Shaper orb, then remove from Atlas. Shape your desired T5 and T6 maps.
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Credits to Karvarousku
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Vendoring maps for upgrades (both regular and shaped) can be see here: https://pathofexile.gamepedia.com/Map#Upgrades
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For example, you can sell Shaped Towers for Underground Sea maps to sell for Vault, which can drop or upgrade to Gorge.
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Vendoring Shaped Maps for hard to acquire Maps:
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T6 -> T7 (T1 Shaper Orb):
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3 Shaped Jungle Valley -> Arachnid Tomb
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T7 -> T8 (T2 Shaper Orb):
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3 Shaped Factory -> Barrows
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3 Shaped Ghetto -> Arena
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Bog can't be 3 to 1'd so be careful with that, can be really aids to get
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T8 -> T9 (T3 Shaper Orb):
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Shaped Vaal Pyramid -> Reef
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Vendoring Maps for Shaper Orbs for T5-T10
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3 Shaped Waste Pool (T4 Shaper Orb) gives Colonnade for T10
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3 Shaped Spider Lairs (T5 Shaper Orb) gives Excavation for T11
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3 Shaped Wharfs (T6 Shaper Orb) gives Estuary for T12
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3 Shaped Ashen Woods gives High Gardens for T13 (can skip if you get an early Oba's unique map unless you want multiple T13s)
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For T14 there's 2 common unique maps that give T14 orbs so don't bother
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3 Shaped Overgrown Shrines gives Overgrown Ruin for T15
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Credits to Karvarousku & Uber