You haven't heard the Tragedy of X4 the Opaque? I thought not. It's not a story Egosoft would tell you. It's a modder legend. Modders are so powerful and so wise they can force X4 to reveal information. They have such a knowledge of the game, they can even play it without Google. Modding is a pathway to many abilities some consider to be unnatural.

The game contains countless mechanics which are fully opaque yet punish the player for not knowing them. These mechanics can only be gleaned by either reading the game code or learning it from someone who has read it.

A hidden mechanic which checks if your mining ships are within 40km of a resource probe owned by you and silently applies a 50% penalty to the final result of the efficiency calculation if they are not. Thus, players are unknowingly hamstrung by this mechanic as there is literally no way to learn it exists in-game.

This mechanic is particularly troubling because vanilla has no automatic method to deploy resource probes, so it's extremely tedious to avoid the penalty without mods. If you know the penalty exists, there is no indication if or when it is applied to your ships. While the game does suggest using probes, the penalty should be removed considering these factors.

Even when using a mod like Satellite Service to automatically blanket the entire sector with probes, it is still possible to receive this penalty because the probes are deployed on one plane. Therefore, you would receive the penalty if the ship moves >40km above or below the probes. Covering the entire sector with probes also reduces performance and visually clutters the UI.

A ship with empty service crew slots further reduces efficiency because they contribute 0 to the combined skill value. Marines do not contribute their skill. Skill value is used for everything and has an enormous impact. Always keep your ships fully crewed.

Known mitigations:
Vanilla — Manually spamming probes.
Satellite Service — Automatically deploys probes, greatly reducing tedium.
No Mining Penalty — Directly removes the penalty.

Using SETA while AFK triggers a hidden penalty which causes your player rank points to decay.

Earning the achievements for player rank is functionally impossible due to the insane logarithmic scaling, but this hidden penalty likely makes it literally impossible.

I don't know the specifics of this penalty because the code is not available to modders.

Source of knowledge:
Developer confirmation on Steam discussion page.

Known mitigations:
Simulating mouse input to prevent AFK detection.

Mining a valuable crystal immediately downgrades all other crystals in the sector into the least valuable type and starts a hidden timer* to prevent any other crystals from spawning.

*Users often claim the timer is 30 minutes, but the code seems to suggest either 60 or 120 depending on the type.

The code documentation states:

Cooldown on "valuable" drops, defined in minutes. If set, collecting one of these will prevent new "valuable" spawns for the defined duration. Entries without a cooldown are considered "not valuable" for the purposes of this cooldown.

Egosoft introduced this penalty to discourage crystal mining, as despite being incredibly boring, it became the early game meta due to being easy and insanely profitable. It was a good idea in theory, but in practice just moved the meta to another badly balanced mechanic and actively harmed players by punishing them with a mechanic they can't know exists.

I don't recommend mining crystals in either vanilla or with the below mods, but you're free to do as you want in your sandbox.

Known mitigations:
Crystal Rarities — Removes the hidden timer and buffs the spawns; very cheaty.
Disable crystal cooldown timer — Removes the hidden timer

Mining activity accumulates a hidden "heat" value which attracts the Kha'ak. Player-owned mining ships build twice as much heat as NPC-owned miners.

Kha'ak "teleport" to any location without the need of travelling through gates. They actually spawn out of thin air, typically right on top of the offending miner's head.

If your miners are under constant attack, it is likely an Outpost has spawned in the sector. There is a separate system independent of Hives and Outposts which infrequently spawns small attacks.

Outposts spawn within 3 jumps of a Hive. Generally the outpost spawns ~400km away from the center of the sector, which is likely beyond the border. However, the hex will zoom out and rescale to accommodate crossing it.

Destroy the Hive before the Outpost. Destroying them will require several destroyers to do it in a reasonable timeframe due to their absurd health pool.

Hives can respawn after 96 hours. Outposts can respawn after 48 hours. The timer is much shorter if player-owned ships do not destroy the station. They do not respawn at the same location within the sector.

The Hives can only spawn in 9 specific sectors, but only 6 of these sectors can contain a Hive.

Since Hives can only exist in 6 of 9 sectors, destroying a Hive might move it to another sector if the local mining activity of the new sector is high enough when it respawns.

The 9 specific sectors are:

• Antigone Memorial
  
• Black Hole Sun V
  
• Company Regard
  
• Heretic's End
  
• Lasting Vengeance
  
• Matrix #451
  
• Open Market
  
• Pious Mists IV
  
• Silent Witness XII

Although it's easy to keep them suppressed with the above knowledge, the entire system is hugely unfun. Kha'ak spawning out of thin air leaves little room for counterplay aside from using L miners. It's also a slog to clear the nests since they spawn so far away and have very little DPS yet enormous health pools.

Known mitigation:
Knowledge
Spawn Begone — Changes Kha'ak spawn mechanics to be less frustrating.
No Kha'ak Torture — Removes the Kha'ak from the game.

A ship's crew only has a chance to bail if their ship's hull and shield are under 75% and 20% respectively. There is a hidden penalty to the bail chance if your ship has higher maximum hull than your target.

Thus, the ideal method is to damage the ship to 74% hull and then keep tickling its shields to keep them under 20% without damaging the hull again, while using a ship which has a maximum hull value equal to or less than your target.

For non-Xenon ships, scan the ship first, then check the crew number every 30 seconds. Once it has 4 crew, the next successful bail roll will cause all remaining crew to abandon ship, thus allowing you to claim the ship. Claiming it transfers ownership to you.

Exact formula:
Vanilla rolls a bail check once every 30 seconds if the target is below 75% hull and 20% shields.
Base eject chance is a range of 23-46%: inversely proportional to crew skill
Multiplied by (targetmaxhull) / (mymaxhull), capped to 1.0
Multiplied by (myshieldperc+myhullperc) / (targetshieldperc+targethullperc), capped to 1.0
Reduced to a quarter if attacker is not personally flown by the player
Reduced to a half if target is capital ship
Reduced to a third if target is Xenon

Known mitigation:
Knowledge
Bail 30s -> 10s — Reduces the tedium of waiting for bails.
No Bail Penalty — Removes maximum hull difference penalty.

Ships sold at player-owned wharfs and shipyards have a penalty on sale price to slow down the snowball into infinite wealth.

The ship price is calculated by:
Cost of components * 5 (with ~15% variance based on supply)

The penalty is 70% when the slider is at 100%. So, even with this penalty, you're making 50% more than the components alone. The penalty is also only 45% when the slider is at 150%.

It would catapult you into infinite wealth far too quickly without the penalty, since selling ships would be 5x more profitable than their components. The profit is also only limited by your production capacity as ships have near infinite demand.

It is therefore a necessary yet poorly communicated bandaid for the unbalanced economy.

Known mitigation:
No Player Shipyard Penalty[www.nexusmods.com] — Lessens or removes the penalty. I don't recommend this mod, but players should be aware of the penalty and decide for themselves.

This list is not exhaustive. Although I've made this other Steam Guide to help other players learn the game, it is difficult to learn these mechanics since they are in fact hidden.

This guide does not include the dozens of factoids which are impossible to learn in-game, as I simply don't have the ability to find, remember, and summarize so many of them.

An example of such a factoid is the effect of defense drones in low-attention. There is a common misconception that they do nothing. It is a reasonable assumption since they are not visually launched and their effect is not indicated anywhere in the UI. However, drones do contribute to the low-attention battle simulation despite giving zero feedback for it. In low-attention, drones both increase the DPS of their owner and absorb incoming damage. The game is unfortunately rampant with this type of hidden information.

Further, it does not include the mountain of mechanics which are unclear or confusing to new players, such as: scrap processor cooldown, pirate cover system, reputation and ranks being a logarithmic scale, scanner tiers for scanning, station budget scaling to storage capacity, sector ownership rules, and so on.