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Does Sonic Stun Gun's effect count for itself?

No, Sonic Stun-Gun doesn't see itself being played.
Source: Aequitas (2020-09-14)    【Link to Ruling】
Tags: Sonic Stun-Gun
What does "being upgraded" mean on Gears’ stratagem Sabotage?

Being upgraded covers any time an upgrade is Put on a character (including Playing, Moving, and Swapping). It does not cover when an upgrade remains on a character during combining.
Source: Aequitas (2020-09-14)    【Link to Ruling】
Tags: Sabotage
What happens if I Reprocess to Scrap an Increased Durability on a character with 3 health remaining?

The Increased Durability is scrapped and the character is then KO'd. As the character is now in the KO area, the repair does not happen.
Source: Aequitas (2020-09-14)    【Link to Ruling】
Tags: Reprocess
Start Your Engines says "Flip each of your characters from bot mode to Car mode". Does this mean that you can target "Car mode" with Precision Fire? Is Car a mode?

No. Car is a trait and not a mode. Despite this card using 'Car mode', you should consider it as a short hand for 'a mode with the Car trait'. The same is true for Hunker Down's use of Tank mode, and Pop a Wheelie's use of Motorcycle mode.
Source: Aequitas (2020-09-14)    【Link to Ruling】
Tags: Start Your Engines, Start Your Engines
For the purposes of Windsweeper's alt-mode ability, is Blitzwing a Plane on your starting team?

No. Your starting team are the visible cards you present to your opponent at the beginning of the game to show you have an acceptable numbers of stars. These are the sides of the cards that show their star cost.

Given this, Blitzwing is a Tank on your starting team unless you are playing the Master Converter stratagem, in which case Blitzwing is both a Tank and Plane on your starting team.
Source: Aequitas (2020-09-14)    【Link to Ruling】
Tags: Blitzwing, Relentless Foe
Can Wolfwire pick up a Paralyzo Box?

Yes. In bot-mode, Wolfwire's ability indicates that instead of the game concept of swapping a green battle icon, Wolfwire can put one in hand. While Wolfwire, with a Melee trait, is unable to swap a card for Paralyzo Box due to its Ranged hybrid green battle icon, it is still a green battle icon and qualifies for his ability.
Source: Aequitas (2020-09-14)    【Link to Ruling】
Tags: Wolfwire, Ground Tracker
If I have 1 damage remaining before a character is KO'd, will Lucky Dodge always work because it can only take 1 damage?

No. A character takes whatever attack damage is applied to it, regardless of how much damage remains to KO the character. Lucky Dodge works on the attack damage being applied to the character, not the actual damage needed to KO them.
Source: Aequitas (2020-09-14)    【Link to Ruling】
Tags: Lucky Dodge
Do Tidal Wave’s deployable 4-stars need to be included in a deck list, or can they be switched out between games independently of the sideboard?

The deployable 4-star characters do not need to be listed in a deck list, allowing different characters to be used in different games. The correct play is for each player to present their starting team to each other, and then the Tidal Wave player fetches their 4-star character, or characters, shows them to their opponent to confirm they are 4 stars or fewer, and places them under the relevant Tidal Wave cards.
Source: Aequitas (2020-09-14)    【Link to Ruling】
Tags: Tidal Wave, Dark Fleet (Aircraft Carrier)
If you play Scouting Mission, and your opponent reveals Reflect Damage, who draws the cards?

The game cares about intent, though we acknowledge that the '->' symbol does not always have the same meaning. In this case, whichever player was targeted for the damage with Scouting Mission is the one that gets to draw the cards, regardless of whether Holomatter Projector or Reflect Damage did something with that damage.
Source: Aequitas (2020-09-14)    【Link to Ruling】
Tags: Scouting Mission
If you send damage at your opponent and they reveal Reflect Damage and send that to a character with a HolomatterProjector, is damage done?

No. Reflect Damage is the source of the reflected damage, so Holomatter successfully blocks that reflected damaage.
Source: Aequitas (2020-09-14)    【Link to Ruling】
Tags: Reflect Damage
If you send Scouting Mission against your own Ulta Magnus Armor, do you draw cards.

Yes.
Source: Aequitas (2020-09-14)    【Link to Ruling】
Tags: Scouting Mission
I attack my opponent's Lord Megatron in bot mode with a character, but I only have one card left in my deck. After reshuffling, I put the damage on the attacking character, KOing it. Do I finish flipping my battle cards for the attack? Does my opponent flip battle cards for their defense?

Yes, you do; and no, they don't. First, while Lord Megatron's bot mode trigger can happen during attack flips, you don't actually resolve it until you have finished flipping for your attack. So you'll flip your last card, reshuffle (triggering Megatron's ability), then complete your attack flips (including any bold or other effects). Assuming you have no triggers yourself dependent on battle flips, Lord Megatron's trigger then resolves, dealing damage equal to his attack to your choice of one of your characters. If this KOs the attacking character, your attack immediately ends. The defending player won't flip cards for defense, and attack damage won't happen
Source: Aequitas (2020-09-14)    【Link to Ruling】
Tags: Lord Megatron, Conqueror of Cybertron
Intrusion Countermeasures Software vs Counterespionage I have a face-down ICS and a second copy in hand. My opponent plays Counterespionage naming ICS. What happens?

Your opponent plays Counterespionage (CS), names Intrusion Countermeasures Software (ICS), and looks at your hand.
As Counterespionage would actually cause you to scrap the copy of ICS you have in hand, we assume you reveal the copy you have in play. ICS then resolves and makes it impossible for your opponent to scrap the ICS in your hand. Instead that part of the effect is replaced by the card drawing effect, and you draw two. This is because the effect of a secret action resolves when the card is revealed, and does not depend on whether the card remains in play or not.
Source: Aequitas (2020-09-14)    【Link to Ruling】
Tags: Intrusion Countermeasures Software
Does a card that refers to Bot Mode apply to a Titan Master (Head + Body mode)?

No. A character in Body mode is not also in Bot mode.

This means that cards like Escape Route do not flip a Body mode character to Alt mode. For an example of a card that works with both Body mode and Bot mode characters, look at how Mission Briefing explicitly says 'in bot mode or body mode'.
Note that cards like Start Your Engines and Hunker Down do not flip the characters from Body mode to Alt mode, however if the characters have Car and Tank traits respectively, they still get the secondary effects of those cards.
Source: Aequitas (2020-09-14)    【Link to Ruling】
Tags: Head, Body
Topspin doesn't have any stars on his card, can I play him for free?
No. That was a printing error. Topspin is a 9-star card.
Source: Aequitas (2020-09-14)    【Link to Ruling】
Tags: Topspin, Air & Space Assault