Elspeth saw that neither available outcome resembled victory. Allowing Jace to finish risked sending the Sylex through the connected branches. Stopping him without removing the weapon left its energy inside the Seedcore. She chose the one destination the plan had not prepared: she took the Sylex herself and carried it away.
The blast vanished with her into the Blind Eternities. To those left behind, Elspeth appeared to have traded her life for worlds that might never know what she prevented. Her act interrupted the weapon but did not undo the losses already suffered. Jace, Nissa, Nahiri and Vraska remained in Phyrexian hands, and Realmbreaker still stood.
Elesh Norn therefore began the invasion with a compromised but functioning network. The assault had damaged New Phyrexia, armed its defenders with knowledge and preserved the Multiverse from an indiscriminate explosion. It had not closed the door. The next war would be fought everywhere at once.
Her intervention is physical, not merely a disagreement. As energy gathers inside the Sylex, Elspeth arrives, drives her sword through Jace and takes the device from his hands. She planeswalks away with it rather than allowing its detonation at the roots of the invasion tree. Jace falls wounded; Elspeth's destination, and whether she can survive the choice, remain unknown to those still in the Seedcore.