1 Place the main board in the middle of the table, with the side showing the artwork you prefer.
2 Place the Influence board nearby.
3 Join the left 3a and right half 3b of the Sequence board and place them nearby.
4 Place the Resource tokens 4a, Shield tokens 4b, Damage markers 4c, Discovery Data cubes 4d, Voidborn ships 4e, and Corruption markers 4f in a common supply.
5 Separately shuffle the three types of Operation cards (Cadet cards 5a, Frigate cards 5b, and Command cards 5c) into three face-down decks.
6 Shuffle the Hidden Influence cards into a face-down deck.
7 Create the Scanner offer above the main board:
7a Find the 15 Scanner cards appropriate to the player count (1-2, 3, or 4), showing the icons
,
, or
on their backs, respectively. Return the remaining 30 cards to the box.
7b Randomly reveal three Scanner cards showing a
(1) on their back into the offer, and return the two other cards with this icon to the box.
8 Form two face-down Scanner decks above the main board from the Scanner cards showing
(2) 8a and
(3) 8b on their back, shuffling each separately.
9 Shuffle the Colony cards into a face-down deck nearby.
10 Place the Rift die appropriate for the number of players next to the Scanner deck, and return the other two dice to the box:
10a 1-2-player game: yellow die
10b 3-player game: orange die
10c 4-player game: dark red die
11 Place the Revenant in the center.
12 Place 1 random Arkship in Sectors 1, 4, and 6, then 2 random Arkships in Sectors 3 and 7.
13 Place 1 random Fighter in every sector except Sector 4. If a Fighter has the same House flag as an Arkship in the same sector, swap the Fighter with the one in the clockwise next sector.
14 Place 1 random Dropship in every sector except Sector 6. Do not check their House flags against other ships.
15 Place Voidborn ships on each sector of the main board, depending on the number of players. See the table below.
16 Place a Rift in Sectors 1, 3, 5, and 7.
17 Shuffle the Planet cards into a face-down deck, then draw and place the top cards face-up in sectors depending on the number of players.
17a 1-3 player game: Sectors 2, 5, and 8.
17b 4-player game: Sectors 2, 4, 6, and 8
18 Place a Discovery Data cube on each revealed Planet card.