During the Siege of Lothal in 4 BBY, Darth Vader, the Sith Lord, orchestrated an attack against Phoenix Squadron. Vader, aiming to track the Spectres to the larger rebel group, set a devious trap. He then personally assaulted the Phoenix fleet in his TIE Advanced, devastating their forces and crippling the rebel command ship Phoenix Home. Thanks to the quick actions of Hera Syndulla and a fortunate distraction caused by Ahsoka Tano, the commander and crew managed to evacuate the damaged Phoenix Home. The remaining rebels then retreated into hyperspace just before Imperial reinforcements arrived.
The Spectres embarked on a mission to the planet Lothal the day preceding the battle to extract Maketh Tua, a defecting Imperial Minister. During this rescue, Tua met her death, and Agent Kallus of the Imperial Security Bureau framed the rebels for her murder under Darth Vader's orders. With their transport destroyed, the rebels found themselves stranded in Lothal's Capital City, lacking local support. Adding to their woes, the Galactic Empire had established a blockade around the planet, seeking to capture them.
In hopes of seizing an Imperial vessel capable of hyperspace travel, the rebels infiltrated the Imperial Complex located in Lothal's Capital City. Inside, they discovered an Imperial shuttle along with several shield generators. Recognizing the opportunity to steal both, they began loading the generators onto the shuttle when Darth Vader and a small contingent of stormtroopers confronted them. The Sith Lord casually dueled the group's two Jedi, Kanan Jarrus and Ezra Bridger, while the stormtroopers engaged the other rebels. After a brief skirmish, the rebels successfully loaded the shield generators and departed. Kanan and Ezra, realizing they were no match for Vader, disengaged and boarded the escaping shuttle. Vader, having orchestrated the entire scenario, allowed their departure without interference.
Unable to escape the planet without alerting the Imperial fleet, the Spectres sought assistance from Lando Calrissian. The galactic entrepreneur arranged for his droid W1-LE to aid their escape by using sensor buoys to mimic their shuttle's signal, thereby dispersing the Imperial fleet. The Spectres successfully bypassed the blockade and rejoined the Phoenix Cell's fleet in deep space. However, Vader had secretly planted a tracking device on the shuttle, intending to follow them back to the Phoenix fleet.
Upon meeting up with the Phoenix fleet, the astromech droid Chopper detected a transmitter on the Spectres' shuttle. Realizing they were being tracked, the Spectres quickly boarded the rebel fleet's command ship Phoenix Home to warn Commander Jun Sato and Ahsoka Tano of the impending danger. However, before any action could be taken, Darth Vader emerged from hyperspace in his TIE Advanced and rapidly approached the rebel fleet. In response, Commander Sato deployed the RZ-1 A-wing interceptors of Phoenix Squadron. Yet, Vader's unmatched piloting skills allowed him to swiftly decimate the squadron.
After breaching Phoenix Squadron, Vader launched a devastating assault against Phoenix Home. With the rebel pilots clearly outmatched and the command ship in grave danger, the Spectres, accompanied by Tano, boarded their VCX-100 light freighter Ghost in an attempt to aid the struggling Phoenix Squadron. Despite the Ghost's assistance, the battle remained overwhelmingly one-sided. Vader continued to bombard Phoenix Home while effortlessly eliminating rebel fighters. He quickly crippled Phoenix Home and destroyed most of the rebel fighters, largely ignoring the Ghost. As he prepared to deliver the final blow to the rebel command ship, Commander Sato implored the crew of the Ghost to stop him. However, the rebels were unable to inflict any damage on Vader's craft as he closed in. During the pursuit, Tano sensed a strong presence in the Force emanating from the Imperial fighter's pilot and decided to combine her abilities with Kanan's to probe the pilot's mind. As they reached out, Ezra Bridger experienced a chilling sensation similar to his encounter with Vader on Lothal, deducing that the pilot was the Sith Lord they had faced before. Simultaneously, Tano managed to glimpse Vader's identity as her former master, Anakin Skywalker, but was overwhelmed by the psychic backlash and collapsed in horror. Vader, in turn, sensed the identity of the mind probing him, realizing that his former Padawan was still alive.
Upon learning of Tano's presence aboard the Ghost, Vader ceased his attack on Phoenix Home and engaged the Ghost. After annihilating the few remaining rebel fighters, Vader began firing upon the Ghost in an attempt to disable it. This diversion allowed Commander Sato and the crew of Phoenix Home to begin evacuating the doomed ship. As the battle drew to a close, several Star Destroyers under the command of Admiral Kassius Konstantine entered the system. Aboard the Relentless, Konstantine contacted Vader for orders. Vader instructed him to position his Star Destroyers to block the Ghost's escape but to refrain from firing, as he wanted the rebels aboard alive. With Vader and the Star Destroyers focused on the Ghost, Sato and his crew successfully abandoned Phoenix Home and escaped the system with the remnants of the Phoenix fleet.
As Vader continued his assault on the Ghost, Hera Syndulla piloted the ship directly towards the Star Destroyers. Following Vader's instructions, the Relentless activated its tractor beam to capture the Ghost as it passed between it and another Star Destroyer. However, Syndulla skillfully navigated through the gap just before the tractor beams became active, causing Vader to be caught instead of the Ghost. The Ghost jumped into hyperspace, and due to the tractor beams, Vader was unable to give chase.
Following their close call with the Empire, the Phoenix and Spectres had to confront the loss of their command ship and the near annihilation of Phoenix Squadron's pilots. Despite facing overwhelming odds, the Spectres resolved to continue aiding the rebellion. Ahsoka, having regained consciousness, was questioned by Ezra about Vader's identity. Consumed by guilt and anguish upon learning of Anakin's fate, Ahsoka lied to Ezra, claiming she had no idea who he was. Meanwhile, Darth Sidious was pleased to learn of Tano's discovery, believing she would lead them to more Jedi. Under Sidious' command, Vader dispatched another Inquisitor to hunt down the rebels.
Due to the heavy losses sustained by the Phoenix fleet, Ahsoka sent the Spectres on a mission to Seelos to find an old ally. This ally turned out to be the former Clone Captain "Rex," who agreed to provide the rebels with information about Galactic Republic military bases in the Outer Rim Territories and on Mandalore. After repelling an Imperial assault, Rex agreed to join the rebellion and accompanied the rebels back to the Phoenix fleet.
The attack on the Phoenix fleet was initially featured in the one-hour movie Star Wars Rebels: The Siege of Lothal, which premiered at Celebration Anaheim on April 18, 2015. It was later broadcast on Disney XD on June 20, 2015.