Act 2 Overview — Super Mario: Roots of Ruin

Click links signified with "→" to view a more detailed summary of a section's plot, including cutscene scripts.

Entering Valley's End

Mario steps foot into Valley's End and bears witness to the true effects of the Umbral Deluge for the first time.
He is somehow trapped within the valley shortly after entering. The MushPhone has trouble functioning while here.
He makes his way towards the Survey Team Hideout, visiting Grapey Gloomscape, Radish Rave, and other areas ravaged by the Deluge along the way.

Once at the hideout, Cachely installs a modification in the MushPhone that restores its capabilities to full. This is the same tech that allowed her to relay the distress signal to the Research Center at the start of the game.
In order for Sagetoad and the others to reach the Survey Team, Mario must help bore a tunnel between Spinach Settlement and the far edge of the hideout, allowing safe travel between the two locations going forward.

After the tunnel is completed, everyone devises a plan to take on the Rogue Sapling:

Mario leads the frontal assault alone, keeping the Sapling occupied and distracted.
Toadprentice, Toaderstudy, and Sagetoad focus magic at several key points at the base of the Sapling to weaken its overall power.
Cachely, Croak, and Blarvey remain at the hideout, monitoring Deluge levels and warning the others of any anomalies.

During the fight, the Rogue Sapling periodically delivers fragmented, cryptic warnings against its own destruction. So much of its cognitive energy is spent controlling the Deluge that it struggles to form intelligible speech.

After the Sapling's defeat, an enormous shockwave releases throughout Gearonia and Deluge spores rapidly disperse from the area. The Deluge shows no signs of fading, a shock to everyone, since the Sapling was believed to be its epicenter and source.
Luigi is freed, but was dangerously close to entering Stage 2 of the Deluge's influence.
After more deliberation, it's deduced that the Rogue Sapling was acting as a vacuum for the Deluge rather than its source. Its motives remain unclear, but it was significantly slowing the outward spread of the corruption. Its actions can only be interpreted as sacrificial heroism, a realization that shocks everyone.
Everyone who contributed to the Sapling's defeat is devastated and remorseful. They return to the hideout to regroup. The next steps are entirely unclear.