There are two large card trays. These have no base and are intended to remain in the game box. The trays have space for sleeved cards and the card dividers. The mail large card tray is again with no base and should stay in the game box. All card slots are designed for sleeved cards and for the game's card dividers. This tray also stores the yellow breach tiles.

The last of the card trays is an unusual tray for Folded Space in that it is stored on its side in the box. The tray does have a base, and has space for sleeved cards. The card dividers do not fit this tray, but in any event we recommend using it for the crystal cards only, making it clear what it contains.

When used with the Aeon's End: Outcasts® version of the game the channel in the top of the card trays can be used to store the two small boards. The insert inside the Pegasus Spiele edition of Aeon's End® has the tray layout being slightly different, and extra pieces are added to two trays to allow for the larger box. Two card trays have extra wall pieces added to one end, which can also function to store the breach tiles freeing up space for more cards. The third tray is a filler tray to fill the box corner.

When clearing the game away and packing the box, all the trays and mats are placed followed lastly by the rule books. This fills the box to the top and allows for vertical storage of the game.