Star Trek: Discovery has finally revealed where the Enterprise was during the Klingon War. The Enterprise may be destined to become the flagship of the United Federation of Planets, but it actually sat out the Klingon War in Star Trek: Discovery season 1, with the Federation refusing to recall Captain Pike and his crew. That decision clearly didn't sit comfortably with Pike, and in season 2 he clashed several times with Starfleet Admirals over whether or not the Enterprise should have been called back.
In one key scene, Vice Admiral Cornwell explained to Pike there was a simple reason she hadn't ordered the Enterprise into the fray. She believed the battle against the Klingons was a defining moment for the Federation, and feared the Federation's decisions would compromise its morality. As such, in her view it was imperative the captain she most trusted was guaranteed to survive in order to serve as the voice of reason, representing the very best ideals of the Federation.
As logical as Cornwell's argument may be, Star Trek: Discovery's latest official tie-in novel has revealed there were other reasons Pike and his crew weren't recalled. John Jackson Miller's The Enterprise War explains just what the USS Enterprise was doing while the Federation was at war. It also reveals the Federation had plans for the Enterprise - plans that suggest just how badly the war was going.
At the time the Klingon War broke out, the Enterprise was exploring the Pergamum Nebula, one of the most hostile areas in space, which stood near the intersection of routes popular with civilian prospectors. The ship had undergone a major refit in order to chart the Pergamum, with a wealth of experimental technology installed into its systems, neatly explaining why Discovery's Enterprise looked a little different. Even with all these modifications, though, the Enterprise was largely out of contact with Earth, with background levels of radiation only occasionally dropping to levels where long-range communication was possible. Pike didn't even learn about the Klingon War until two months after the Battle of the Binary Stars.
The Federation swiftly saw an opportunity in Pike's mission, although they initially attempted to hide it from him. Admiral Terral recognized the risk the Federation would lose the war, and he hoped the Enterprise could find an inhabitable world at the heart of the Pergamum, one that could serve as a suitable refuge for humanity. With ships like the Enterprise and the Discovery, the Federation could establish a last colony and live in peace in the Pergamum, safe from the Klingons, who would be unable to pursue them into the nebula. As the war progressed, the Federation gave up on this idea, and simply hoped Pike and his crew could give a legacy to the human race when the Klingons had destroyed Earth. Cornwell sent what she feared would be her final message; "If this goes badly, Chris, make sure people know we were here." Star Trek: Discovery had only hinted things were this bleak, but The Enterprise War makes it clear the races of the Federation believed they were facing extinction at the hands of the Klingons.
Unfortunately, the Enterprise encountered hostile life-forms who lived inside the Pergamum, two races who were locked in a centuries-old war. Even the Enterprise was vulnerable in such hostile terrain, and some of its crew were taken away as slaves while others were stranded on a barren moon. Spock was left isolated, and received a visit from the Red Angel when he was at the point of death. It took Captain Pike the best part of a year to rescue his crew and establish an uneasy peace in the Pergamum. When the Enterprise finally emerged from the nebula, and picked up all the messages it had been sent, the Klingon War was over. Pike could only reflect with sorrow that he believed he could have saved Federation lives had his ship been part of the war effort.