Stop the Stampede
Once you've gotten both herds together underneath the big oak tree, a nearby lightning strike will spook the cattle, sending them sprinting off toward a nearby cliff. Chase after the stampede, pushing your horse as fast as possible to get in front of them before they reach the cliff.
If you catch them in time, the cows will slow down and avoid falling to their deaths. You don't have to save them all to complete the mission, but as many as possible should be saved.
After you've got them stopped, send any stragglers you see on your mini map back to the herd, then ride back to Bonnie at the blue dot on your map. Round up the rest of the stragglers, then start pushing the herd back toward the ranch, taking care of any stragglers that break off from the main group. Remember that you can press "UP" on the D-Pad to get the moving more quickly.
Once you make it to the ranch, push the herd through the gate and into the corral. Once they're all in, the ranch hands will close the gate and Bonnie thanks you for your assistance.
Congratulations, you've saved the herd, gained some honor, and finished the "A Tempest Looms" mission. You've also finished the last of the available Bonnie MacFarlane missions. You'll have to do some work for the Marshal in Armadillo before you come back to the ranch.
For more mission walkthroughs, cheat codes, weapons guides, and more, check out our Ultimate Guide to Red Dead Redemption.