Eventually, Stross attacked and overpowered Ellie, stabbing her in the eye with the screwdriver in an effort to get her to follow “the steps”. Throughout Isaac's journey through the derelict ship, Stross grew increasingly violent toward Ellie, biting and threatening her with a screwdriver. Isaac decided to head back into the Ishimura and activate the ship's Gravity Tethers to pull them toward the Titan Shard by force, while Ellie was left with Stross in the tram again. Isaac entered the Ishimura on his own. Their progression to the Government Sector was hindered following the tram track's destruction by Hans Tiedemann's control over the Solar Array's beam.

Ellie provided Isaac with waypoints to aid in their escape and was eventually able to operate a tram. Despite Stross' increasing dementia and insanity, Ellie was left to guard the scientist whenever Isaac left to clear a path for their escape.

Isaac, Ellie and Stross then decided to band together to escape the Sprawl. In the face of her threats to kill Stross, Isaac convinced her to keep him alive. Despite her distrust of both him and Isaac, she contacted the engineer to let him know that she had found him. Shortly after parting ways, Ellie encountered Nolan Stross. She warned him not to follow her and continued onward. Ellie declined, citing that bringing anyone with her would be “a liability”. Isaac offered his assistance, believing that they could work together. Near the end of the battle, she was discovered by Isaac Clarke on his way to the Transport Hub. Repairing the control panel to an elevator, Ellie was attacked by a swarm of Slashers. She used a security gate to protect herself from the swarm as she wore them down. He tried to kill her, but she managed to escape. At some point during her journey through the Concourse, she encountered an individual who claimed that he wanted to help her. On her own, Ellie struggled to reach the Government Sector, unaware that it was the location of Site 12 Marker.

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