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The Bactrian is indeed an excellent flagship for capturing and plundering. No ship can beat it in crew capacity and only one can beat it in cargo space, the Deep River from the Wanderers. It is generally not effective in combat once you progress much beyond the tier 1 (human) story and so I do recommend removing all weapons from it and giving it a Systems Core to make it less squishy and as for engines, it can perfectly fit the biggest Hai Atomic engines which can makee it quite speedy. You should probably go with cargo on it and use it in conjunction with a fleet of warships to farm the automata in the Core.
Quarg technology is indeed still the best obtainable, apart from the 3 Pug Arfectas it is possible to obtain however it would require you to make them irreversibly angry at you which may impact future story. There is an exploit where you go to the territory of a species hostile to them, in this case, that'd be the Heliarch while you have some of their ships as escorts, this occurs a few times during the tier 2 (Wanderer) story and repair both sides' ships when they become disabled to raise your reputation with that species however you have gone beyond the point where this is possible. It should be noted that a few well outfitted tier 2 (Wanderer, Korath automata) heavy warships are a match for Quarg ships.
The Bactrian is still the best ship you can get for capturing, but if you want a less squishy ship that is also able to capture well, you're going to need to find a ship that isn't as good at capturing as the Bactrian. I would suggest you either capture a Solifuge from the Unfettered Hai attacking the Wanderers or capture a Korath Raider, assuming you don't mind the massive crew requirement. You're only real bet beyond those two ships (which are still rather squishy if compared to something like the 349 even though they're tougher than the Bactrian) is a Quarg Skylark, which is highly difficult to capture but is still doable. The only problem with that is that it will cause the Quarg to become hostile, possibly ruining your chances at doing the last part of the Wanderer campaign when it is released.
Quarg tech is still the best, but as mentioned, once you're hostile you can't go back. All the chances to cheese your reputation with the Quarg to higher than it should be (which allows you to capture or board a single Quarg ship for a lot of grinding) are tied to the story, so they're likely all behind you can this point. But for the future, the way to increase your Quarg reputation is by finding a mission with Quarg escorts and bringing the Quarg to an alien faction that is hostile to them. You can then continually repair the Quarg when they are disabled, raising your reputation.
Also, have you meet what is currently available for coalition and remnant content? The latter gives you a unique opportunity to capture a [worldship].
Species are primarily organized by a tiering system, defined by a recursive relation: a tier X heavy warship is equivalent in strength to a tier X+1 light warship.
We aren't very consistent with this, though.
The hoonams are tier 1. The Korath are tier 2.
The Hai are somewhere in between the hoonams and the Korath.
The Coalition is tier 1.5.
The Korath exiles are between hoonams and the Korath automata.
The Wanderers are in the end more advanced than the Korath automata.
The Heliarchs are tier 2.5 (but use Coalition outfits).
The Quarg are, supposedly, tier 3 (but balance is basically nonexistent with them, so we can't really use them as a completed tier 3 metric).
The Remnant uses technology from so many different tiers that you can't really define one standard tier for them.
The Drak and the Archons are apparently tier 4, but they'll be rebalanced to be the strongest in the galaxy at some point.
The Pug don't have a definite tier, as far as we know.
It's technically obtainable in Korath exile space, but you can't actually bring it out of their space, because there is nowhere to land there to install a jump drive.
The Bactrian is praised not for any real combat prowess (for which it is basically useless, lategame), but for its near-unmatched bunks and cargo space.
The only ship that defeats it is the Korath world-ship, which is itself nearly impossible to obtain because of its ridiculously high bunks.
Yes, Quarg technology is still the best obtainable, excluding the three Pug Arfectas.
The exploit here is to bring Quarg ships (most effectively, mission ships, because they'll come literally everywhere with you) into a hostile space that is a match for them. The typical example of this is bringing the Quarg into Heliarch space, which also lets you increase your reputation with the Heliarchs, although it can also be done with the Kor Mereti (assuming this is pre-Wanderer campaign) or even the pirates (assuming sufficient quantities - that is, probably over a hundred ships).
Once you've brought the ships, just wait around, and eventually the factions will disable each other. Then, board the ships (assuming you're friendly with them), and your reputation is increased.
Note that in 0.9.9, you'll have to do this to be able to capture a Pug Arfecta, because Pug reputation mechanics were changed to a similar fashion as the Quarg.
you can also get archons, but that one you can only get the ship without the outfits
So to summarize, for my flagship, I'm probably going to want to stick to bactrian, because I value both crew capacity and cargo. I apparently missed my unique chance to get a worldship via the remnant storyline, so that's out of the running for now. ramscoops + cloaking works well enough to keep me alive, so I'm going to stick to that and let my fleet do the work. This is assuming I don't want to piss off the quarg or pug.
For my fleet, I'm guessing hurricane seems best then. I'm not sure what a good combination of outfits are. I'm guessing blue sun reactor is good, large heat shunt seems most effecient, large systems core also seems good. Are sunbeams still the best besides skylances? I'm also wanting to implement korath warders, at least one each, into my lineup. I read that deep atomic engines were the best, but has that changed? Oh, and I'm ignoring missile/consumable weapons for my own fleet, because I dislike upkeep as mentioned before.
Cooling modules are actually far more powerful per ton than Korath heat shunts, if you can handle the added energy costs. I actually stick to shunts myself because I don't want to increase my energy costs.
It may be worth looking at hai engines. While they aren't as powerful per ton, they create a lot less heat.
Korath firelances can be a nice alternative to sunbeams for causing heat samage and conserving space, at the cost of raw dps.
Really, it all comes down to your own preferred playing style.
The large heat shunt is indeed the best cooling outfit. Coalition cooling modules are more space efficient, but the energy drain does build up.
The large systems core is definitely the best choice here. It's more space efficient overall once you factor in the energy requirements and the masses of a generator and of a battery. Plus, free hull repair.
Sunbeams are great as weapons, though you'll want something for hull damage. Also consider getting Korath disruptors.
Korath warders are okay, but they drain quite a bit of energy, and they're not much use against the tougher missiles in Korath space.
Consider using Wanderer anti-missiles instead: more energy efficient, smaller, (barely) longer-ranged; and while they fire slower, they pack a punch, which is more valuable against the Korath missiles due to the way the anti-missile mechanic works.
If you want something even better, go for a Remnant point defense turret instead, which is basically a Wanderer anti-missile but with a doubled rate of fire. Note, though, that it has a shorter range, and that it drains much more energy.
Atomic engines used to be the best, but now they've been superseded by Wanderer and Korath engines.
Wanderer engines aren't as powerful as atomic engines, but the energy efficiency and cooling are definitely worth it. Korath engines are basically atomic engines taken to the extreme.
You'll want to use Wanderer engines if you're playing with a Wanderer ship. It's viable because Wanderer ships are already pretty light in general. As for Korath ships, you'll want to use Korath engines unless you want to move at the speed of a space whale, because of their sheer mass.
I would like to know why the heliarch power sources have such absurd price tags while everything else is competively priced for a t2 item.
hull damage? oh look at that, there's different stats for shield vs hull damage. What would you recommend for hull damage?