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Could this be Spinward Fringe Broadcast 0: Origins or one of the Spinward Fringe Series, by Randolph Lalonde? The series are a bit more recent than your timeline, with the first published in 2008, and the above book in 2010, although parts in 2008 under a the titles Firstlight Freeground, Limbo and Starfree Port. You can read part for free on Smashwords Broadcast 0: Origins.

In Broadcast 0: Origins, the main character is a decommissioned officer who is reactivated on the advent of a war, following him (and his friends) hacking into the training software for the military/navy base and playing as combatants. During this he and his friends rise to the top of the training software rankings, showing up experienced commanders.

As a result of his reactivation, he is given command of a re-commissioned spaceship (why he wasn't thrown in jail, I don't know), which has reactive armour, capable of repairing itself following damage and being remodeled to re-shape the ship when needed.

In his command he has one female officer who wasn't part of his friend group, who is young and attractive to him and they develop a relationship early in the second part of the novel.

I don't recall anything about a wormhole, but the ship and crew are sent off on a long-term "unofficial" (my term, perhaps "undercover" is a better term) mission to obtain tech that may be useful in the war. This mission essentially puts them on their own resources and in disguise. I think (may be a different story I read at about the same time) at the end they return to their home base to rescue it from an attack.

It is one of those stories where the ship and crew pull through against impossible odds, but come out fighting and enhance their abilities by adding to their ship and personal armaments/equipment after each engagement.

Could this be Spinward Fringe Broadcast 0: Origins or one of the Spinward Fringe Series, by Randolph Lalonde? The series are a bit more recent than your timeline, with the first published in 2008, and the above book in 2010, although parts in 2008 under a the titles Firstlight Freeground, Limbo and Starfree Port. You can read Broadcast 0: Origins for free on Smashwords.

In Broadcast 0: Origins, the main character is a decommissioned officer who is reactivated on the advent of a war, following him (and his friends) hacking into the training software for the military/navy base and playing as combatants. During this he and his friends rise to the top of the training software rankings, showing up experienced commanders.

As a result of his reactivation, he is given command of a re-commissioned spaceship (why he wasn't thrown in jail, I don't know), which has reactive armour, capable of repairing itself following damage and being remodeled to re-shape the ship when needed.

In his command he has one female officer who wasn't part of his friend group, who is young and attractive to him and they develop a relationship early in the second part of the novel.

I don't recall anything about a wormhole, but the ship and crew are sent off on a long-term "unofficial" (my term, perhaps "undercover" is a better term) mission to obtain tech that may be useful in the war. This mission essentially puts them on their own resources and in disguise. I think (may be a different story I read at about the same time) at the end they return to their home base to rescue it from an attack.

It is one of those stories where the ship and crew pull through against impossible odds, but come out fighting and enhance their abilities by adding to their ship and personal armaments/equipment after each engagement.

Could this be Spinward Fringe Broadcast 0: Origins or one of the Spinward Fringe Series, by Randolph Lalonde? The series are a bit more recent than your timeline, with the first published in 2008, and the above book in 2010, although parts in 2008 under a the titles Firstlight Freeground, Limbo and Starfree Port. You can read part for free on Smashwords Broadcast 0: Origins.

In Broadcast 0: Origins, the main character is a decommissioned officer who is reactivated on the advent of a war, following him (and his friends) hacking into the training software for the military/navy base and playing as combatants. During this he and his friends rise to the top of the training software rankings, showing up experienced commanders.

As a result of his reactivation, he is given command of a re-commissioned spaceship (why he wasn't thrown in jail, I don't know), which has reactive armour, capable of repairing itself following damage and being remodeled to re-shape the ship when needed. In his command he has one woman who wasn't part of his friend group, who is young and attractive to him and IIRC they spend much of the book in a "will-they/won't-they" situation.

I don't recall anything about a wormhole, but the ship and crew are sent off on a long-term "unofficial" (my term) mission to do something (I don't recall what), that essentially puts them on their own resources and in disguise. I think (may be a different story I read at about the same time) at the end they return to their home base to rescue it from an attack.

It is one of those stories where the ship and crew pull through against impossible odds, but come out fighting and enhance their abilities by adding to their ship and personal armaments/equipment after each engagement.

Could this be Spinward Fringe Broadcast 0: Origins or one of the Spinward Fringe Series, by Randolph Lalonde? The series are a bit more recent than your timeline, with the first published in 2008, and the above book in 2010, although parts in 2008 under a the titles Firstlight Freeground, Limbo and Starfree Port. You can read part for free on Smashwords Broadcast 0: Origins.

In Broadcast 0: Origins, the main character is a decommissioned officer who is reactivated on the advent of a war, following him (and his friends) hacking into the training software for the military/navy base and playing as combatants. During this he and his friends rise to the top of the training software rankings, showing up experienced commanders.

As a result of his reactivation, he is given command of a re-commissioned spaceship (why he wasn't thrown in jail, I don't know), which has reactive armour, capable of repairing itself following damage and being remodeled to re-shape the ship when needed. 

In his command he has one female officer who wasn't part of his friend group, who is young and attractive to him and they develop a relationship early in the second part of the novel.

I don't recall anything about a wormhole, but the ship and crew are sent off on a long-term "unofficial" (my term, perhaps "undercover" is a better term) mission to obtain tech that may be useful in the war. This mission essentially puts them on their own resources and in disguise. I think (may be a different story I read at about the same time) at the end they return to their home base to rescue it from an attack.

It is one of those stories where the ship and crew pull through against impossible odds, but come out fighting and enhance their abilities by adding to their ship and personal armaments/equipment after each engagement.

Could this be Spinward Fringe Broadcast 0: Origins or one of the Spinward Fringe Series, by Randolph Lalonde? The series are a bit more recent than your timeline, with the first published in 2008, and the above book in 2010, although parts in 2008 under a the titles Firstlight Freeground, Limbo and Starfree Port. You can read for free on google books: Broadcast 0: Origins and possibly others in the series.

In Broadcast 0: Origins, the main character is a decommissioned officer who is reactivated on the advent of a war, following him (and his friends) hacking into the training software for the military/navy base and playing as combatants. During this he and his friends rise to the top of the training software rankings, showing up experienced commanders.

As a result of his reactivation, he is given command of a re-commissioned spaceship (why he wasn't thrown in jail, I don't know), which has reactive armour, capable of repairing itself following damage and being remodeled to re-shape the ship when needed. In his command he has one woman who wasn't part of his friend group, who is young and attractive to him and IIRC they spend much of the book in a "will-they/won't-they" situation.

I don't recall anything about a wormhole, but the ship and crew are sent off on a long-term "unofficial" (my term) mission to do something (I don't recall what), that essentially puts them on their own resources and in disguise. I think (may be a different story I read at about the same time) at the end they return to their home base to rescue it from an attack.

It is one of those stories where the ship and crew pull through against impossible odds, but come out fighting and enhance their abilities by adding to their ship and personal armaments/equipment after each engagement.

Could this be Spinward Fringe Broadcast 0: Origins or one of the Spinward Fringe Series, by Randolph Lalonde? The series are a bit more recent than your timeline, with the first published in 2008, and the above book in 2010, although parts in 2008 under a the titles Firstlight Freeground, Limbo and Starfree Port. You can read part for free on Smashwords Broadcast 0: Origins.

In Broadcast 0: Origins, the main character is a decommissioned officer who is reactivated on the advent of a war, following him (and his friends) hacking into the training software for the military/navy base and playing as combatants. During this he and his friends rise to the top of the training software rankings, showing up experienced commanders.

As a result of his reactivation, he is given command of a re-commissioned spaceship (why he wasn't thrown in jail, I don't know), which has reactive armour, capable of repairing itself following damage and being remodeled to re-shape the ship when needed. In his command he has one woman who wasn't part of his friend group, who is young and attractive to him and IIRC they spend much of the book in a "will-they/won't-they" situation.

I don't recall anything about a wormhole, but the ship and crew are sent off on a long-term "unofficial" (my term) mission to do something (I don't recall what), that essentially puts them on their own resources and in disguise. I think (may be a different story I read at about the same time) at the end they return to their home base to rescue it from an attack.

It is one of those stories where the ship and crew pull through against impossible odds, but come out fighting and enhance their abilities by adding to their ship and personal armaments/equipment after each engagement.