¶ Overview
There are currently 9 possible operation modifiers. Every 10 | Super Helldive operation has 2 UNLESS the planet is on Defense Campaign where all mission have 0 modifiers (except in Megacities.
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3 are general
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1 is Automatons exclusive
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2 are Terminids exclusive
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1 is Illuminate exclusive
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2 are Megacity exclusive
¶ All Factions
¶ Complex Stratagem Plotting
What it does: Stratagem call-in time increased by 50%
Select this modifier for run?: NO
Effect on speedrun: Probably the most damaging modifier for a speedrun, avoid it at all costs!
The extraction counts as a stratagem and will be increased from the default 2m to 3m (without the Expert Extraction Pilot booster). This means up to an entire extra minute will be added to your run which you can do nothing about.
Additionally, the time spent waiting for stratagems to activate will be increased which can add time to your run in cases such as Destroy Command Bunkers or Blitz: Search and Destroy.
¶ Orbital Fluctations
What it does: Stratagem cooldown increased by 25%
Select this modifier for run?: Yes
Effect on speedrun: Usually neglible so long as you budget your red stratagems properly.
Virtually no effect on blue stratagems other than Expendable Anti-Tank and Commando. All multiplayer runs are short enough (less than 10m) to the point where higher cooldowns don't make a difference.
However, repeatedly using Eagles will be negatively impacted somewhat (+2s waiting in between uses) which can add a few seconds onto certain outpost clears.
¶ Poor Intel
What it does: Hides exact location of objectives on map, instead displaying a radius similar to the Eliminate missions.
Select this modifier for run?: YES
Effect on speedrun: Basically a freebie if you pre-scout and annotate a map with the real location of objectives.
Not that impactful even without pre-scouting as true objective locations are easily determined by just looking at structures either on the map or environment.
Red splotches and pre-revealed sides on the preview also have inaccurate placement, but display normally after drop.
¶ 
Automaton only
The best modifiers for Automatons are:
- Orbital Fluctations
- Poor Intel
Gunship Patrols are not that bad either, especially if you can bring a Rocket Sentry.
¶ Gunship Patrols
What it does: Large groups of gunships spawn at edges of map and move across map to the other side in a patrol pattern. Patrols have less gunships in singleplayer.
Select this modifier for run?: Yes, but have a plan to deal with them.
Effect on speedrun: They can be very annoying especially if you have to hold a position to complete a subobjective/main objective but their impact on time can be mitigated through planning and/or teamwork. Explosive and Plasma weapons can destroy them. The most reliable pick is the Rocket Sentry.
In order to deal with these effectively, all players should call out patrols, giving info of their location, number and direction of travel.
Next, the team must decide whether to avoid or engage the patrol.
If avoiding, stay out of the red searchlight to avoid detection and avoid making noise or using red stratagems in the flight path, as this will send the gunships into search mode.
In this clip here you can see I am right underneath the gunship but remain undetected due to not making any noise and staying out of the searchlight.
¶ 
Terminid only
The best modifiers for Automatons are:
- Orbital Fluctations
- Atmospheric Spores (if pre-scouted)
- Roving Shriekers (if un-scouted)
¶ Atmospheric Spores
What it does: Map obscured by yellow hazy spore effect, hiding side objectives, POIs, and bug outposts until they are discovered. Can be difficult to view terrain outline as well, but not impossible.
Select this modifier for run?: Yes (if pre-scouted)
Effect on speedrun: Basically the inverse of Poor Intel (sides hidden instead of main).
Freebie with pre-scouting, but unlike Poor Intel is very damaging to un-scouted runs since it is much harder to discover all the optional objectives and outposts compared to main objectives, and there is no hints given whatsoever as to their location.
Worth noting that it is possible to create map markers in game for outposts even though the icon is hidden if you simply click where the outpost would be after discovered.
Icon is fully displayed for optional objectives so no workaround needed for creating map markers.
Note that this modifier disables radar and pings from the Scout armor passive.
¶ Shrieker Patrols
What it does: Large groups of shriekers spawn at edges of map and patrol to the other side of map in a similar manner as gunship patrols.
Select this modifier for run?: Yes, if your primary weapon can handle them or if you can bring a Machine Gun Sentry.
Effect on speedrun: Pushovers for certain primaries, but can be deadly for others or in certain situations. Machine Gun Sentry is a very reliable pick against them.
They can also repeatedly flinch you off of terminals which can be very annoying and lose you time.
¶ 
Illuminate only
¶ Leviathan Blockade
What it does: Up to 5 Leviathans will appear beyond the mission area.
Select this modifier for run?: NO
Effect on speedrun: Leviathans can see you from extremely far away, even if no other enemies have detected you and regardless of whether you are wearing a Scout armour.
Although they have been through many nerfs, their shots can be deadly in light armor and cause considerable time/stim loss due to the repetitive ragdolls.
They cannot be killed as easily as Stingrays, Shreikers, or Gunships. They are time, stress, and resource drains.
¶ Megacity only
¶ Civilians & SEAF in Area (Defense only)
What it does: Super Earth civilians will randomly appear fleeing from enemies. SEAF soldiers will randomly appear fighting enemies.
Select this modifier for run?: Yes
Effect on speedrun: The effects are very RNG because you can't predict when they'll appear or how they'll behave.
Civilians can attract enemies and this can divide aggro. The same goes for SEAF soldiers, but with the additional benefit of being able to fight them, which can get you out of a bad situation or clear the way for you.
¶ SEAF Units in Area (Liberation only)
What it does: SEAF soldiers will randomly appear fighting enemies.
Select this modifier for run?: Yes
Effect on speedrun: The effects are very RNG because you can't predict when they'll appear or how they'll behave.
SEAF soldiers can attract enemies and this can divide aggro. They can fight them as well, which can get you out of a bad situation or clear the way for you.
¶ Credits
Helldivers Wiki for some assets and information.