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Flag in Exile consists of a prologue, 34 chapters, and an epilogue.
Admiral Hamish Alexander, Earl of White Haven, leads the Royal Manticoran Navy's attack on the Nightingale System. As the People's Navy approaches, his ships fire missiles, causing terrible destruction, but the Havenites also score hits, destroying the superdreadnought HMS King Michael. When a second enemy force lights up its impeller wedges, White Haven realizes he walked into a trap, and orders his force to engage the first force before retreating. Deep inside, he realizes that the war has just changed, as the Havenites have stopped a Manticoran offensive dead for the first time.
Chapter One Edit
High Admiral Wesley Matthews, supreme commander of the Grayson Space Navy, visits the Protector's Palace for a private audience with Protector Benjamin IX. They meet in the monarch's flower garden, where Matthews asks the Protector's permission to involve Honor Harrington in the organization of the rapidly expanding Navy. Benjamin IX is concerned that the Steadholder has still not recovered from the death of her lover, Paul Tankersley, but the High Admiral explains that Manticore is losing momentum in the war against Haven. Soon the RMN will have to pull its last capital ships out of the Yeltsin's Star System, and the GSN will then have to defend it on its own. He thus wants Harrington to serve as a loan officer in the Grayson Navy.
Chapter Two Edit
Honor Harrington relaxes in her swimming pool, something that still seems bizarre to her Grayson armsmen, who come from a society that would never "waste" clean water in such a way. She discusses a upcoming dedication ceremony and the fact that there will be protests against her with Major Andrew LaFollet. Knowing that none of these protesters will ever understand the depth of her agony over losing Paul, she assures LaFollet that the protests will not be a problem.
Chapter Three Edit
After watching her treecat Nimitz playfully hunt a Sphinxian chipmunk through the garden, Honor goes to meet with her regent, Howard Clinkscales. As they walk back into the house, they notice some protesters outside the premises. Clinkscales and LaFolett are outraged by the disrespectful placards they carry, but Honor orders them to leave them be.
However, once the Steadholder turns her attention to some paperwork, the Major quietly instructs armsman Simon Mattingly to find some loyal Grayson Sky Domes construction workers to "take care" of the protesters.
Chapter Four Edit
While her personal maid, Miranda LaFollet, helps her into her wardrobe, Honor thinks about the way she slowly becomes aquainted with Grayson fashion, even though she still refuses to wear the over-the-top costumes common among upper-class Grayson women.
Chapter Five Edit
Honor's car makes its way through Harrington City to Bernard Yanakov Park, as she considers the changes that Adam Gerrick's new crystoplast domes will bring to Grayson society and economy. When she arrives for the dedication of the Yountz Center at the center of the park, she notices a number of protesters, but many more loyal steaders.
As the ceremony proceeds, Honor informs her subjects that Grayson Sky Domes has received construction commitments worth over two hundred million austins now that the first crystoplast domes are finished. At the following buffet, Brother Edmond Marchant, personal chaplain of the conservative Steadholder Burdette, steps forward and accuses Honor of leading her people to damnation. Honor counters his arguments, surprising him and everyone else with her detailed knowledge of Grayson scripture. When Marchant calls her a "harlot" about her extramarital relations with the late Paul Tankerley, the crowd turns fully against him, and Honor has to order her Guard to protect Marchant from the angry mob ready to lynch him.
Chapter Six Edit
Some time later, Honor is busy with sword practice when High Admiral Matthews is announced. He bluntly tells her that he wants her to accept an officer's commission in the Grayson Space Navy, and counters every argument she has against it. She even questions her very ability to command, but Matthews assures her of his trust in her, and also states that the Navy desperately needs her and her expertise.
Honor eventually agrees, and Matthews points out that the refitted superdreadnought GNS Terrible will be ready for her soon. Astonished, she points out that she has never commanded a capital ship before, but the High Admiral realizes there has been a misunderstanding: Terrible is to be her flagship when she takes command of the GSN's First Battle Squadron -- as Admiral Harrington.
Chapter Seven Edit
Robert Stanton Pierre, chairman of the Committee of Public Safety and nominal leader of the People's Republic of Haven, ponders the changes that his star nation underwent since the fall of the Legislaturalist regime and his own rise to power. Even though his takeover has rocked the system, he is uncertain wether there is still time to save the corrupt Republic from certain doom.
Realizing that when even his modest attempts at reform fail, the mob may soon turn onto him and his Committee, he approves the execution of two large-scale military operations, Stalking Horse and Dagger.
Chapter Eight Edit
Four days after the events in Yanakov Park, Honor attends mass at Harrington Cathedral, where Reverend Hanks denounces Brother Marchant's actions. He reads a public edict removing Marchant from the rectory of Burdette Cathedral as well as from the office of Lord Burdette's chaplain, and stripping him of all ranks and offices.
On the way home, Honor observes a group of men with wooden clubs heading to Yanakov Park, and quickly orders Major LaFolett to call the police and Guard to prevent a violent riot. The major is confused for a moment, then begins to laugh uncontrollably. The men, he explains, are carrying bats used for an ancient team sport called baseball. Shocked that his Steadholder has never heard of it, he points out that it is Graysons' favorite sport, and every steading has a team. He then proceeds to explain the game to her.
Chapter Nine Edit
Admiral Lady Dame Honor Harrington, Grayson Space Navy, meets with her new flag captain, and is surprised to find that he is none other than Captain Alfredo Yu, the exiled commander of the late Havenite cruiser PNS Saladin, now in the service of the GSN. Her chief of staff is with him, and to her delight turns out to be Captain (JG) Mercedes Brigham, also on loan from the RMN. As they make their way up to the Terrible in a pinnace, Honor wonders wether she will ever be able to fully forgive Yu for all the lives lost during her first assignment to Yeltsin's Star. Just then, the captain brings the point up and offers her to have him replaced. He also explains that he has become a Grayson citizen since transferring to the GSN two years earlier, intent on never returning to Haven.
Honor asks him to let her think about his offer for a while as the pinnace approaches her new flagship.
Chapter Ten Edit
Honor admires the view of GNS Terrible, the largest and most powerful ship she has ever served on, then the pinnace settles into the boat bay. Captain Yu introduces her to her staff and the ship's senior officers, including her staff chaplain and flag lieutenant, two experiences that are new for her. She then inspects her quarters, which are luxurious even by Manticoran standards.
Honor and Captain Brigham discuss their past adventures at Yeltsin's Star as well as the following occupation of Masada. Brigham explains that the planet is even more backwards than expected, and the way women are treated is a hundred times more barbaric than on Grayson. Since Manticore took over, the murder rate is on the rise, with numerous wives killing their husbands in retribution for a lifetime of pain and subjugation. The Captain actually transferred away from Masada because she couldn't bear being around its people any more.
Chapter Eleven Edit
At a staff meeting, Honor and her officers discuss the upcoming withdrawal of the last Manticoran ships of the wall from Yeltsin's Star. Soon the GSN will have to defend the Protectorate of Grayson on its own, and there is a lot of training and reorganization coming up for its officers.
Vice Admiral Alexander Thurston of the reformed People's Navy discusses some delays in Operation Dagger with his People's Commissioner Michael Preznikov, who represents the mighty Office of State Security. As one of the few senior officers to survive the Committee of Public Safety's purges, Thurston is fully aware that he has to be careful around the Citizen Commisioner, who lacks any military experience and hardly understands their operational plan. However, the political officer surprises him by strongly supporting his recommendation to keep future delays to the operation to a minimum.
Chapter Twelve Edit
While Admiral Harrington is busy with war games to get her battle squadron in shape, Lord William Fitzclarence, Steadholder Burdette, meets Deacon Allman, who informs him that the Sacristy has refused his petition to reinstate Brother Marchant. The Steadholder reacts by challenging the Church's authority in the matter.
Chapter Thirteen Edit
While evaluating the performance of her division commanders, Honor becomes disappointed with herself for her inability to forgive Captain Yu, especially considering what a highly competent officer and good man he has proven to be in the past weeks.
John Mackenzie, Steadholder Mackenzie and Samuel Mueller, Steadholder Mueller, meet with Lord Burdette in his private library over a glas of wine. They discuss their unsuccessful attempts to weaken Steadholder Harrington and the Protector, and Burdette insists that they must employ more radical means. Lord Mackenzie is uncomfortable with the direction in which the conversation is heading, and excuses himself. Once he is gone, Brother Marchant, who is also present, notes that if mortal men err in their service to God, other men must be ready to correct these errors.
Lord Burdette considers Benjamin IX's restoration such an error, and he has a plan to correct it...
Chapter Fourteen Edit
On her way to a dinner at the Protector's Palace, Honor thinks about the continuing protests and the rising resistance against the Mayhew reforms by a number of conservative steadholders led by Lord Burdette.
The Protector and his family welcome Honor and Nimitz, with the Mayhew daughters being especially delighted to have time to play with the treecat. As they make off with him, Benjamin IX explains to Honor that the last RMN units will soon leave the system to reinforce Admiral White Haven after his defeat at Nightingale. One squadron from the Manticoran Home Fleet is due to pass through Yeltsin in time for some exercises.
They also discuss the problem of Marchant and Burdette's growing influence, but the Protector is sure that Honor is exactly the ally he needs to weather this crisis.
Chapter Fifteen Edit
Vice Admiral Esther McQueen and the Havenite Task Force 30 conquer the Minette System, while Vice Admiral Diego Abbot and Task Force 20 do the same thing in the Candor System, depriving the Manticoran Alliance of two of its members.
Chapter Sixteen Edit
Protector Benjamin IX and Chancellor Henry Prestwick are informed that Lord Burdette has placed his new chaplain under house arrest and returned Brother Marchant to Burdette Cathedral's pulpit on his own authority. He questions the Protector's as well as the Sacristy's right to remove Marchant from his position in the first place.
Samuel M. Harding works as a power bore operator at the Grayson Sky Domes construction site at Winston Mueller Middle School in Mueller Steading. His co-workers are unaware that he actually sabotages the project by causing slight discrepancies in the holes bored into the superstructure, thus making sure that the dome will eventually collapse. In fact, the company does not even know his real name, and is thus unaware that his mother's maiden name was Marchant.
Chapter Seventeen Edit
Honor is busy with batlle exercises against Admiral Alfred Henries' Manticoran battle squadron when news of the taking of Minette and Candor arrives at Yeltsin's Star. Everyone assembles aboard the High Admiral's flagship, where they discuss the detaileds of the recent attacks. Wesley Matthews then countermands Admiral Henries' standing orders and sends him to the Casca System together with his own Battle Squadron 2 to reinforce the front against an attack from the lost systems and, if possible, retake Candor. Honor is to remain behind to guard Yeltsin's Star.
Chapter Eightteen Edit
Commander Warner Caslet of the light cruiser PNS Vaubon once again reminds his tactical officer, Lieutenant Shannon Foraker, to observe the proper rules about addressing other officers as "Citizen", lest their People's Commissioner, Denis Jourdain, becomes displeased with her. As they patrol the hyper limit of the Casca System, they get confirmation that a large number of ships of the wall has arrived from Yeltsin, and retreat to report this development.
Chapter Nineteen Edit
Honor dines with her chaplain, Abraham Jackson, and they discuss Brother Marchant's campaign against her, as well as Manticorans' and Graysons' different attitudes towards state religions.
Adam Gerrick, lead engineer and minority shareholder of Grayson Sky Domes, inspects the new dome erected above Winston Mueller Middle School. He is extremely happy with his work and the wealth it brough him, but while observing the dome, he suddenly notices a loose support beam, and before he can do anything about it, one of the dome's panels drops on the schoolchildren below.
Chapter Twenty Edit
Honor Harrington sits in her quarters, shocked by the terrible accident that cost the lives of eighty-two people, including thirty children, their teachers, and a number of her own employees. She remembers the agony in Adam Gerrick's face when he told her, and feels the same deep guilt he does.
Gerrick tries to get involved in the investigation of the accident, desperate to find out if the same thing could happen to other projects, but the inspector angrily refuses and orders him and his men of the premises under threat of shooting them.
Protector Benjamin watches footage of the incident, and is informed by the Chancellor that the laboratories have identfied substandard ceramacrete samples in the rubble. He realizes that this will lead to a whole new wave of anti-reform protests, possibly stronger than ever before.
Steadholder Burdette is shocked by what their conspiracy has led to, but Brother Marchant assures him that everything that happened was God's will.
Gerrick meets with Howard Clinkscales and his colleague Frederick Bennington, who assures him that all components delivered to the Mueller project were according to regulations. Gerrick quickly concludes that somebody must have replaced the materials on-site, and makes it clear that he will do whatever he can to prove it and find the saboteur.
Chapter Twenty-One Edit
Rear Admiral Thomas Theisman arrives for a staff meeting of Task Force 14, overseen by Vice Admiral Alexander Thurston. They discuss the newest information about Grayson units having arrived in Casca, and Admiral announces that Operation Dagger, a large scale assault on Yeltsin's Star and Endicott, will launch in 72 hours.
Just like Protector Benjamin had feared, the release of the forensic report about the Mueller Middle school disaster has led to widespread protests and brought Grayson Sky Domes' construction projects to a total halt. The crisis has the potential to completely bankrupt Honor Harrington, her company, and her steading.
Adam Gerrick's team eventually discovers what made the dome collapse, and that all faulty bore holes were drilled by the same person, the operator of Power Bore Number Four.
Chapter Twenty-Two Edit
Four hours later, Gerrick arrives at Harrington House to bring his findings to the attention of the Steadholder: that the Mueller dome was sabotaged by drilling wrong holes which, together with the bad ceramacrete, could not hold the weight of the superstructure. These holes were drilled by a man named Lawrence Maguire, who it turns out used an assumed name; he did however, have a run-in as a teenager, so Planetary Security was able to identify his fingerprints: he is actually Samuel Marchant Harding, a cousin of Brother Edmond Marchant and a resident of Burdette Steading.
Chapter Twenty-Three Edit
The Protector and the Chancellor inform Reverend Hanks about the sabotage and Brother Marchant's apparent involvement in it. The head of the Church is shocked, but also fears that Lord Burdette will make the evidence disappear once an official investigation is started. And they have to act soon, as more and more steadholders are demanding a murder trial against Lady Harrington. Benjamin IX decides to summon a closed session of the steadholders to give them enough information to refrain from a trial against Honor. Reverend Hanks goes to get Honor and Adam Gerrick, who are still aboard the Terrible.
At the same time, Rear Admiral Theisman's staff keeps training for the attack on Yeltsin's Star.
Chapter Twenty-Four Edit
When the summons to the secret session arrives, Steadholder Mueller begins to make preparations to make sure his involvement in the sabotage of the Mueller dome will never be discovered. Marchant, meanwhile, advises Steadholder Burdette to use the few contacts he has left in the Ministry of Justice following the "Mayhew Restoration" to find out if the government is suspecting anything.
As Minister of Justice Aaron Sidemore begins his official investigation, Reverend Hanks arrives aboard Terrible to deliver the Protector's writ of summons to Honor, as well as his request to bring Adam Gerrick along.
Chapter Twenty-Five Edit
As his ships make their way into hyperspace for the journey to Yeltsin, Rear Admiral Theisman considers the fact that he will soon face Honor Harrington in battle once more.
Lord Burdette has learned from his sources that Lady Harrington knows about the sabotage. He and Brother Marchant realize that they only have a chance of getting out of the affair alive if Honor Harrington and Adam Gerrick never get a chance to present their findings to the Conclave.
Chapter Twenty-Six Edit
Honor and Gerrick are on their way to the surface in a pinnace, accompanied by her flag lieutenant and Reverend Hanks.
Edward Martin, a devout former Burdette Steadholder's Guard soldier, prepares to make a great sacrifice to convince the Church of the wrongness of Lady Harrington's ways. As her pinnace approaches, he and his partner Austin Taylor enter the Harrington Space Facility and kill a guard who tries to stop him.
Moments later, when the dead guard is discovered by his relief, the alarm is sounded. Marting and Taylor fire a surface-to-air missile at Honor's pinnace, which her pilot tries to dodge by shutting off the engines diving straight for the ground.
Chapter Twenty-Seven Edit
The missile hits the pinnace's nose, killing the flight deck crew instantly and causing the vessel to crash to the ground. Honor orders her armsmen to get Adam Gerrick off the wreck while she helps the Reverend, but Armsmen Yard and Candless drag her away while Major LaFollet takes care of Hanks. Once they are safe LaFollet and Yard go back for Gerrick. However, before they arrive, the pinnace explodes, killing Gerrick and many rescuers who had hurried to the scene.
Martin and Taylor try to kill Honor by shooting her, but Nimitz notices them and kills Taylor. Reverend Hanks throws himself in the way of Martin's fire, sacrificing himself to save Honor.
Jamie Candless prepares to execute Martin, who is in agony when he realizes whom he just killed, but Honor tells him that they need the assassin alive. Candless then knocks him out with his pulser's butt.
Chapter Twenty-Eight Edit
News of the events at Harrington Space Facility spreads all over the planet, without any sure information about Steadholder Harrington's fate. Lord Burdette once again finds himself horrified by the consequences of his actions. Meanwhile, Lord Mueller orders an officer of his own Guard to get his men in position in Burdette.
Edward Martin is questioned by Jeremiah Sullivan, Second Elder of the Church of Humanity Unchained, and Protector Benjamin himself. Fearing that the murder of the Reverend will condemn his immortal soul to hell for all eternity, he makes a full confession.
Chapter Twenty-Nine Edit
The Conclave of Steadholders is assembled in the ancient hall of the Conclave Chamber. Benjamin IX enters without being challenged by the Door Warden, which a Protector does only to pass judgement upon one of the men inside. He announces that a member of this house has committed a crime even worse than that of Maccabeus years before: the sabotage of the Mueller dome to discredit Steadholder Harrington, as well as the murder of Adam Gerrick and Reverend Hanks. The Conclave erupts in horror of this revelation, as the Protector reveals that the First Elder's sacrifice saved Lady Harrington.
At this point, Honor Harrington enters the Chamber, still wearing the marks of the recent attack, and demands justice from the Protector. She accuses William Fitzclarence of all the aforementioned crimes and more, and demands his life as satisfaction.
Lord Burdette does not deny his acts any more, but states that they were righteous and necessary, and demands trial by combat against the Protector's Champion. That office is, of course, held by Honor, who gets confirmation from Benjamin IX that Lord Burdette is not to leave the Chamber alive.
Confident that his decades-long training with the Grayson katana will help him win, Burdette attacks Honor, but she has become a well-trained swordswoman herself by now, and easily slices him open and decapitates him.
Chapter Thirty Edit
Honor makes her way back to Terrible. Once there, she feels Captain Yu's relief that she is alive through Nimitz, and finally accepts that they are enemies no more. Honor decides to go to sleep.
Hours later, Vice Admiral Thurston's task force drops out of hyper and makes its way for the inner Yeltsin System. Even though she is in pain and tired after recent events, Honor leads the Grayson Space Navy as it prepares for battle against the invaders.
Chapter Thirty-One Edit
Honor observes that she has the heavier ships even thouth the enemy outnumbers her own forces, but that the enemy still seems to be coming in for a regular engagement using their battleships and lighter units. It suddenly dawns on her that the Havenites are unaware that there are still superdreadnoughts left at Yeltsin's Star; they believe all capital ships have travelled to Casca, and now come in to destroy the orbital fords around Grayson.
Honor then decides to meet the enemy in a surprise attack.
Chapter Thirty-Two Edit
Vice Admiral Thurston's staff finally spots a Grayson formation comming towards them, consisting of battlecruisers and smaller units. This is because Honor is carefully hiding her superdreadnoughts behind the lighter units' impeller wedges.
Thurston orders Rear Admiral Theisman's task group to break off and head for Endicott, a movie Theisman is not entirely sure about, but obeys nonetheless. Honor is delighted by the move, since it devides her enemies into two groups.
Aboard the Vaubon, Lieutenant Shannon Foraker notices something odd about the Graysons' formation, and Commander Caslet quickley realizes that it is a wall of battle -- something a group of battlecruisers would never form in this situation. He reports it to Vice Admiral Thurston, who realizes to late that he faces a force of superdreadnoughts.
Honor orders her screen to scatter and the squadron to rotate for battle.
Chapter Thirty-Three Edit
The Grayson force falls into position at nine million kilometers distance, and its superdreadnoughts and the numerous missile pods they towed open fire on the heart of the enemy formation. They hit to terrible effect, destroying eleven battleships, including Vice Admiral Thurston's flagship, PNS Conquistador.
The Havenite return salvo destroys six of Honor's nineteen battlecruisers, then concentrate all their fire on the Grayson superdreadnoughts. GNS Glorious explodes in space as her sister ships reach energy weapon range, and their broadsides make short work of the remaining battleships and battlecruisers. What history will know as the Fourth Battle of Yeltsin's Star ends with a single Havenite ship fleeing past the Grayson wall of battle. Honor has lost one superdreadnought and several other ships, as well as over 20,000 crewmen, but the Havenites' losses are much, much worse.
However, Commander Frederick Bagwell reports that the other Havenite formation has cut its acceleration to zero.
Chapter Thirty-Four Edit
After witnessing Admiral Harrington's destruction of Thurston's ships, Rear Admiral Theisman orders his task group to go after her, hoping to take her out now that she is weakened.
Honor's staff suggests they return to the protection of Grayson's forts, but Honor points out that the Havenite force was likely bound for Endicott to reinforce the Masadans -- something they can not allow to happen.
The two forces head towards each other, their commanders trying to interpret each others moves. Honor suddenly has an idea, and contacts Captain Mark Brentworth, who remains at the outskirts of the system with eight battlecruisers, via FTL.
When the signatures of a number of Manticoran superdreadnoughts suddenly appear in the system, People's Commissioner LePic orders Theisman to break off the attack and escape to the hyper limit.
As the Havenites are driven away by the false superdreadnought emissions created by Captain Brentworth's recon drones, Honor's staff cheers as she has once again won the day. The admiral finally goes to her quarters and falls sound asleep within minutes.
Chancellor Prestwick gives a report of the battle to the still assembled Conclave, and Steadholder Mueller is the first to stand and applaud, while secretly cursing Honor Harrington. His agents have already gotten rid of almost everyone involved in the Mueller dome conspiracy, with Samuel Harding's death looking like a suicide and Brother Marchant apparently having been lynched by an angry mob.
He then promises to repay any damage done to Grayson Sky Domes, and petitions the Conclave to reimburse the company and Lady Harrington for all legal costs stemming from litigation due to recent events. As a final gesture, he recommends to append the Crossed Swords to her Star of Grayson, effectivly awarding the medal a second time, an honor that only Isaiah Mackenzie, Benjamin the Great's lead general in the Civil War, has received so far. The current Steadholder Mackenzie seconds the motion, and the Chamber erupts in applause for Honor Harrington.