The Box was a seamless, violet contianer with a DNA response system, so that it could only open when touched by a certain individual.
Mira sent Leah to inflitrate Terra Nova and retrieve the box. She found it hidden under the floor of Karem and Selena McMillen's home, which used to be Mira's. However, she was caught before she brought the box back to Mira, and the box was stored in the Clinic, so that it could be examined by Malcolm Wallace. ("The Runaway") After the Sixers used an Empirosaur as a diversion, they were able to escape with the box. Mira delivered it to Lucas, who successfully opened the container. This revealed projections of equations, similar to those he had painted on the rocks near the waterfall. ("Nightfall") The equations were later revealed by Commander Nathaniel Taylor to be a part of an attempted recreation of formulas created by Lucas, after the originals were destroyed. The formula somehow allowed one to open a portal that led from the past to the future. ("Vs.")
The use for the box is finally discovered when Lucas Taylor uses it as a remote control to manipulate the portal. ("Within") He then uses it to travel back to 2149 through Portal Terminus.
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