Within the Jedi cruiser Resolute, Anakin Skywalker and Admiral Yularen brief the assembled clone pilots of Shadow Squadron on their strike mission against the Malevolence. Anakin believes a small squad of Y-wing bombers could outmaneuver the enemy vessel's ion cannon and target its bridge, knocking out the ship and General Grievous.

In the Ryndellia system, the Malevolence continues its assault against the Republic, blasting apart a convoy of medical frigates. Even escape pods are targeted for annihilation.

When word of Grievous' assaults reaches Anakin, he predicts the cyborg general will next attack the Kaliida Shoals medical station. A nearby nebula limits the Malevolence's hyperspace capabilities, which allows Shadow Squadron to get ahead of the warship. Plo Koon decides to join Anakin's squadron in his Jedi starfighter.

At the Kaliida Shoals station, the Kaminoan chief Nala Se receives a warning from Admiral Yularen. She cannot evacuate all the wounded from the station before Grievous' predicted attack. Obi-Wan Kenobi plans to arrive at the station to provide assistance with his cruiser, Negotiator.

The Y-wings fly through the Kaliida nebula through a short cut called the Balmorra Run. Entering the dust cloud blocks the fighters' scanners. Ahsoka grows worried about this dangerous course of action.

In the heart of the nebula, Shadow Squadron suddenly stumbles upon a flock of giant neebray mantas. The annoyed hulks begin to swim around the Y-wing fighters, and Anakin orders evasive maneuvers. Shadow Two (Matchstick) grazes a neebray wing as he flies by, causing damage to his portside thruster stabilizer. The fighters emerge from the nebula, where the neebrays will not follow.

The Malevolence emerges from hyperspace and is swarmed by Anakin's squadron. Grievous launches vulture droid fighters. A group of medical transports flee the Kaliida Shoals station, and Grievous targets them with an ion blast.

When Grievous targets Shadow Squadron with an ion blast, Anakin orders his fighters to fly to the edge of the incoming blast. Shadow Two's crippled stabilizer blows, and he spins out of control, plowing into another Y-wing. Three other fighters fail to outrun the ion blast and are immobilized. Anakin is now down to almost half his original squadron, possibly not enough for him to continue his mission.

The rest of the Y-wings close in on the Malevolence, but another fighter is blown from the skies. Ahsoka urges Anakin to come up with a new plan. Anakin realizes his Padawan is right: he gives up trying to destroy the bridge and General Grievous, and instead targets the ion cannon.

The remaining fighters of Shadow Squadron change course, and fly toward the ion cannon. They fire proton torpedoes into the cannon, causing it to explode in a blast that rocks the Malevolence, and disrupts the massive ship's hyperdrive.

Just then, Obi-Wan Kenobi's taskforce emerges from hyperspace. The Negotiator continues pursuit of the Malevolence while Anakin's Y-wing fighters head to the medical station. Docked at the medical station hangar, Plo Koon congratulates Anakin on his successful run.