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In TOS, TNG, Voyager, the movies and early seasons of DS9 we see great ship–to-ship battles that last multiple phaser / torpedo hits.

In the starship series, we often here Worf / Tasha / Tuvok say "Shields down to 58% captain".

However during the Dominion War in the über-battles such as the second battle for DS9 we see Cardassian, Romulan, Federation, Klingon and Jem'Hadar ships get taken out with one or two shots.

The only in-universe explanation I can think of is the advent of Quantum Torpedoes which could nullify traditional shields and shield technology hasn’t caught up with this yet.

I know that out-of-universe, a battle where each ship can take 20 phaser / torpedo hits is not as exciting as a Galaxy class ship exploding from one hit but I am looking for an in-universe explanation please.

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I think one possible explanation is that in main plots of the various series, what we are seeing in the episodes week to week are the strongest, newest and most advanced ships of the time. The Enterprise 1701 was the flagship. The Enterprise 1701-D was the flagship. The Defiant was an almost new design built for battle. And the Voyager was new and one of the "most advanced ships in the fleet".

In war time, you put out every ship you can get your hands on. Old ships limited to system patrol or convoy escort are now thrown into the battle lines with battle cruisers. 35 year old ships are dragged out of storage and "mothballs", given some minor upgrades and sent out to fight alongside the brand new dreadnoughts.

In war, you use every resource you have available. And the older, weaker ships don't last nearly as long in a fleet combat as the newest ones would.

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    We should also bear in mind that the Dominion were apparently more technologically advanced than the Alpha Quadrant species, albeit not by a lot. They had limited resources and were still comfortably winning the war until the Romulans switched sides. Then the addition of the Breen led to them hitting their stride again, until the Cardassians defected. – James Sheridan Apr 3 '14 at 21:37
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    +1 also, the Galaxy class starship in The Jem'Hadar takes one helluva beating before it is rammed and destroyed – HorusKol Apr 3 '14 at 23:03
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Out-of-universe, shields in ST (or, really, any other sci-fi universe) last precisely as long as the plot requires, and not a nanosecond more. If it builds tension, Worf can shout about the shields being down to 58% after a sustained volley lasting half the episode; if it gives us impressive visuals or shows that the characters on other ships are in peril, the (now-ex) tactical officer can simply forget to raise the shields altogether. (Pretty, though!)

In-universe, you have to realize that we almost never see an unbroken shot of even a single ship going from pristine condition and full energy reserves to glowing cloud of plasma. Our view bounces from ship-to-ship, from exterior to interior and back again -- and even when the ships aren't on our television screens there's still a war being fought. You may have only seen that ship over there take one or two phaser hits before it exploded, but in the realities of war those could have been the fiftieth and fifty-first hits this battle, to say nothing of yet-unrepaired damage it may have suffered in previous engagements.

(Edit to add: There's also numerous occasions where we see weapons fire but do not see where it winds up, such as phaser blasts and photon torpedoes flashing across a viewscreen, but without a corresponding sound or shutter indicating the ship whose view we're sharing was hit. Sure, many of these could simply be misses ("Evasive maneuvers!" and all that), but equally many could hit and damage ships we later see exploding.)

Further, there really is a mis-match in ship classes in many of these engagements -- Jem'Hadar fighters, for example, simply don't have the size to even carry shield systems powerful enough to counter the multiple phaser banks of, say, a Constitution-class starship -- each individual bank dwarfing the size of the fighter! Ships such as these are only a threat due to their numbers, as is mentioned several times throughout these episodes.

All this on top of what BBlake points out, that during most of the shows we're following Starfleet's greatest achievements in master shipbuilding -- but in a war there will be everything from today's greatest pinnacle of tech to slag heaps that were obsolete last century. Especially if it's a war you've been losing, where you're having to pull out every last resource you can muster just to survive one more day against insurmountable odds. (Just ask Poland, who tried to resist the German armored division's Blitzkrieg with cavalry -- and yes, I do mean the man-riding-a-horse kind!)

And, finally, you can't forget the point James Sheridan also makes above, which is that the Dominion did have a technological edge, so it only makes sense that their ships (and, perhaps to a lesser extent, those of their allies) would have less trouble punching through even the best shields going up against them.

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In addition to the other explanations, it’s worth considering that the “great ship–to-ship battles that last multiple phaser / torpedo hits” may have different tactical considerations than the big battles we see in DS9.

When you’re taking on another ship on your own, one mistake by you could result in your destruction and the entire failure of whatever mission you’re on, whereas in a big battle there are other ships around to continue the fight, and lots of enemy ships that you ideally want to take out.

One-to-one battles may therefore be conducted more defensively by both combatants, and thus result in the ships surviving for longer than they would in a larger battle. Note that the battle to re-take Deep Space Nine from the Dominion appeared in an episode called “Sacrifice of Angels”.

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