This story is collected in:

X-Wing Rogue Squadron Omnibus: Volume 3

Comic Book series published August thru November 1998 as X-Wing Rogue Squadron #32, 33, 34 & 35 by Dark Horse Comics:

Synopsis:
When Imperial Intelligence chief Ysanne Isard discovers that acting-Emperor Pestage has made a deal with the Rebel Alliance, it appears that the Rebels' ticket to Imperial Center has been punched. But a Rebel operative witnesses Pestage's capture, and Rogue Squadron is assigned to go after him.
Their rest and relaxation over, Rogue Squadron and a Rebel task force descend on the world where Sate Pestage, one-time Emperor-proxy, has gone into exile. If the New Republic wants to claim Imperial Center for themselves and turn the tide of the war, it is imperative that they rescue Pestage, wanted by the Empire for high treason.
The Rogues stage a dangerous rescue of Sate Pestage. Now is their chance to undermine Ysanne Isard, who has her own designs on the Imperial throne. But a power struggle in the Empire's highest circles has Isard cornered, and that's when the Imperial Intelligence Chief is most dangerous!
As Rogue Squadron prepares for a nightmare showdown against Imperial fighters and ground troops, Isard begins her own personal war in the corridors of power on Imperial Center. A war fought with hidden bombs, double-crossing servants, and knives in the back!

Synopsis taken from Dark Horse Comics, www.darkhorse.com.

Related Stories (in chronological order):

• Rogue Squadron 1/2 by Michael A. Stackpole et al.
• A New Hope
• The Empire Strikes Back
• Return of the Jedi
• The Truce at Bakura
• Lucky by Rob Williams et al.
• Rogue Leader by Haden Blackman et al.
• Rogue Squadron Special by Ryder Wyndham et al.
• The Rebel Opposition by Michael A. Stackpole et al.
• The Phantom Affair by Michael A. Stackpole et al.
• Battleground Tatooine by Michael A. Stackpole et al.
• The Warrior Princess by Michael A. Stackpole et al.
• Requiem for a Rogue by Michael A. Stackpole et al.
• In the Empire's Service by Michael A. Stackpole et al.
• The Making of Baron Fel by Michael A. Stackpole et al.
• Family Ties by Michael A. Stackpole et al.
• Masquerade by Michael A. Stackpole et al.
• Mandatory Retirement

The following novels are sequels to the above stories, and are set from 6 years after the Battle of Yavin during the period of The New Republic, in chronological order:

• Rogue Squadron by Michael A. Stackpole
• Wedge's Gamble by Michael A. Stackpole
• The Krytos Trap by Michael A. Stackpole
• The Bacta War by Michael A. Stackpole
• Wraith Squadron by Aaron Allston
• Iron Fist by Aaron Allston
• Solo Command by Aaron Allston
• Isard's Revenge by Michael A. Stackpole
• Starfighters of Adumar by Aaron Allston