MTG Salvation

Under C.R. 205.1a, if an effect removes the creature card type from an object (such as in the case of Kruphix), any creature types are also removed from it, but only "for the entire time the object's card type is removed." And since Unstable Shapeshifter (which has become a copy of Kruphix) has regained the creature card type, it also regains the God creature type, since the creature card type is no longer "removed".

If you exile the Vehicle that's a creature with Identity Thief's ability (assuming it's a nontoken permanent), you still return that card to the battlefield even if it isn't a creature card ("the exiled card" on the delayed triggered ability refers to the card exiled due to Identity Thief's ability, regardless of its nature [C.R. 607.2a]).

If a noncreature non-Vehicle permanent becomes an artifact creature due to the crew ability, its power and toughness will be undefined, so are treated as 0/0 (C.R. 107.2). If a noncreature Vehicle becomes an artifact creature due to the crew ability, it will "immediately ha[ve] its printed power and toughness" (new C.R. 301.7b), so they won't be undefined.

EDIT (Jan. 5): Added rules basis for second paragraph.
EDIT (Jul. 19): Struck out certain text in second paragraph.

Note that players don't have priority while a spell or ability is resolving (C.R. 116.2e). Thus, for example, no player has priority to cast spells (such as Tread Upon) to raise the targeted creature's power and toughness while Harnessed Lightning resolves (C.R. 116.1a), but rather, a player can respond to that ability only before it resolves, at the latest, so without knowing whether you will pay energy counters due to Harnessed Lightning (C.R. 116.7).

EDIT (Mar. 23, 2018): Correctness edit.

Assuming that you and your opponent are the only players still in the game and no player responded to Fateful Showdown, the game would be a draw. You finish resolving Fateful Showdown, then check state-based actions (C.R. 116.3b, 116.5). Since your opponent has 0 life (C.R. 704.5a), and you tried to draw a card from an empty library (C.R. 704.5b), you both lose the game simultaneously (C.R. 704.3). And if all players still in the game lose simultaneously, the game is a draw (C.R. 104.4a). (Note that the spell's effects don't happen "at the same time"; rather, they are followed in the order given [C.R. 608.2c].)

The Unstable Shapeshifter, which is now Kruphix—

• would remain legendary and an enchantment, and
• would remain a God assuming that under C.R. 205.1a, the phrase "for the entire time the object's card type is removed" is intended to mean "for the entire time the object doesn't have that card type" (so that Unstable Shapeshifter's creature types won't be removed since Unstable Shapeshifter remains a creature; but see, for example, this submission on Reddit.).

An effect that makes a permanent an "artifact creature" without specifying creature types doesn't remove its supertypes, subtypes, or other card types (C.R. 205.1b, 205.4b; review the crew ability at C.R. 702.122a).

Because Unstable Shapeshifter became a copy of Kruphix before it became an artifact creature, it will be a creature irrespective of Kruphix's abilities. (The effect that made Unstable Shapeshifter become a copy of Kruphix and therefore acquire Kruphix's first ability [C.R. 707.2, 613.7a] has an earlier timestamp than the effect that made it an "artifact creature" [C.R. 613.7b]; since both effects change card types [C.R. 613.1d], and neither depends on the other [C.R. 613.8a], they are applied in timestamp order, so the latter effect will override the former [C.R. 613.7].) When a permanent becomes a copy of a creature, it also acquires the latter's power and toughness from its copiable values (C.R. 707.2), so in this scenario, Unstable Shapeshifter's power and toughness will be 4/7 (they won't be those of the exiled card; in any case, Myr Welder's second ability refers only to that card's activated abilities, not its power and toughness).

EDIT (Jan. 12, 2017): Added citation to C.R. 702.121a, which is new to Kaladesh.
EDIT (Jan. 19, 2018): Clarification.
EDIT (Oct. 1, 2019): Edited to conform to rule change with Throne of Eldraine.
EDIT (Feb. 11, 2022): Some rules were renumbered in the meantime.
EDIT (Jul. 3, 2022): Correctness edit to first part of this comment.
EDIT (Jul. 11, 2022): Add link to Reddit submission.

Only permanents that Imprisoned in the Moon can enchant can be selected (so not those with protection from a quality shared with Imprisoned in the Moon [C.R. 702.16c, 702.16i]). Thus, if Progenitus can't be selected because it has "protection from everything", you must select, if possible, another "creature, land, or planeswalker" that could be enchanted by Imprisoned in the Moon (C.R. 303.4f; this applies in this case because Copy Enchantment didn't resolve as an Aura spell). In general, only if there is nothing to enchant does the copying Imprisoned in the Moon not enter the battlefield (and will go the graveyard if it tried to enter from the stack) (C.R. 303.4g).

You will still lose all but 1 life when Soulgorger Orgg's enters-the-battlefield ability resolves, even if another player controls Soulgorger Orgg at that moment. This is because you controlled Soulgorger Orgg when it entered the battlefield (C.R. 112.8) (so the "you" in the ability will refer to you [C.R. 109.5]), and triggered abilities, "[o]nce ... triggered", "exis[t] independently" of their sources (C.R. 112.7a).

EDIT (Feb. 15, 2018): Correctness edit.

The Commander variant doesn't explicitly change the maximum size of the sideboard, which is 15 cards in constructed play (C.R. 100.4a, 903). (Nothing in the rules for the Commander variant [as given in C.R. 903] explicitly precludes the use of sideboards.) EDIT (added after comment 5 was posted): Although the Commander variant (as defined in the comprehensive rules) does not explicitly preclude the use of sideboards, neither are they required by the comprehensive rules (C.R. 100.4 says that "each player may also have a sideboard").

Note also that under C.R. 100.6a, "[a] multiplayer match usually consists of only one game". Since sideboards are used to modify decks only "between games of a match" (C.R. 100.4), it's generally useless for players to have a sideboard in a multiplayer match.

Athreos's ability triggers only if a creature you own "dies", that is, goes to the graveyard from the battlefield (C.R. 700.4). But if your commander would go to exile or your graveyard, hand, or library from the battlefield, you may choose to move it to the command zone instead (C.R. 903.9), including if it would go to your hand while Athreos's ability resolves (again, provided it "dies", is a creature you own, and makes that ability trigger).

EDIT (Jan. 18, Apr. 9, Apr. 22): Clarification.
EDIT (Apr. 26): Added a paragraph after the first one.
EDIT (Aug. 6, 2018): Correctness edit.
EDIT (Jul. 2, 2020): Edited to conform to rule update with Core Set 2021.

In general, an ability that triggers when you cast a spell will go on the stack above that spell (C.R. 405.2), so will get to resolve before that spell (C.R. 116.4). Therefore, the damage from Kozilek's Return can be dealt only before Distended Mindbinder resolves, so Distended Mindbinder won't be affected by that damage (Distended Mindbinder is a "creature" only while it's on the battlefield [C.R. 109.2]).

Note also that you don't "activate" Kozilek's Return (that card has no activated abilities, but rather a triggered ability); rather, you choose to exile it from your graveyard when its triggered ability resolves, not when you put the ability on the stack (C.R. 603.5).

In a multiplayer game, when a player leaves the game, control of the permanent reverts to its previous controller, assuming you did not own that permanent (C.R. 800.4a). If only two players were still in the game and a player loses, the game is simply over; the game would end either in a draw or in a win for the other player, depending on the circumstances (C.R. 104.2a, 104.4a).

(Note that Commander is a variant that's independent of the multiplayer variants and options in effect in the game; nothing in the rules for that variant [under C.R. 903] explicitly precludes applying those rules to two-player games [C.R. 903.2].)

EDIT (Apr. 23): Correctness edit in last paragraph.

If an effect ends the turn (from Time Stop, for example), the triggered ability that would cause the card to be played will be exiled (C.R. 716.1b) and won't trigger again until the next moment that the last time counter is removed from that card (C.R. 603.2) (because Jhoira's effect that grants suspend has no duration, so it lasts for the rest of the game [C.R. 611.2a]). However, since a card must have a time counter on it (in addition to being exiled and having the suspend keyword) to be "suspended" (C.R. 702.61b), it won't be affected by effects that affect "suspended cards".

EDIT (Apr. 18): Added rule citation.
EDIT (Jul. 18, 2018): One rule was renumbered with Dominaria.

Suspend's last ability triggers when the last time counter is removed from the suspended card, whether or not it's your upkeep (C.R. 702.61a). When that ability resolves, the suspended card (here, Jokulhaups) is played if able (even if it isn't your upkeep), and it doesn't matter whether it's a sorcery because the card is played at a moment that cards normally can't be played (for spells, the rule is C.R. 608.2f; for lands, you follow the "play" keyword action under C.R. 608.2c and 701.13, but see C.R. 305.2b, 305.3). Moreover, Jokulhaups doesn't restrict when it can be cast (compare with Savage Beating; a spell's card type, such as sorcery, doesn't impose such a restriction [C.R. 116.1a]).

EDIT (Sep. 21): Made correction.
EDIT (Sep. 30): One rule was renumbered with Kaladesh.
EDIT (Dec. 25, 2017): Add rule citations.
EDIT (Jul. 24, 2018): One rule was renumbered with Dominaria.

The only way the outcome will change in your scenario is if you let Essence Flux resolve as you describe (assuming you own and control the other Spirit creature) and you have Mausoleum Wanderer's triggered ability trigger as a result and resolve, all while Mausoleum Wanderer is still on the battlefield. Otherwise, the X on Mausoleum Wanderer's activated ability will still be 1 when you activate its ability (because that was its power at the last moment it was on the battlefield, when you sacrificed it to pay that ability's cost).

EDIT: Edited just after comment 7 was posted.

X will be Mausoleum Wanderer's power at the last moment it was on the battlefield (so just before you sacrificed it) (C.R. 112.7a). After you sacrifice Mausoleum Wanderer with its ability, when Essence Flux resolves to exile and return the other Spirit creature you control (even if you own that creature), Mausoleum Wanderer won't be on the battlefield anymore to trigger its second ability (C.R. 112.6).

EDIT: Edited just after comment 7 was posted.

Quote from bhas2zhin »

But it says whenever. So as long as a player casts a spell, it will trigger. If in a turn there were 4 spells that was cast, he should have at least 4 counters.

The triggered ability could use "When ..." rather than "Whenever ...", and its meaning wouldn't change as far as the game is concerned, and the same would apply if the ability used, say, "At the time..." (a formulation not used to begin any triggered ability in the Oracle card reference) rather than "Whenever ..." (C.R. 603.1).

The behavior with Aetherflux Reservoir doesn't apply to all triggered abilities, which do no more than what they say.

Managorger Hydra's ability triggers only once for each spell cast (C.R. 603.2c), and for each such ability that resolves, you put only one +1/+1 counter on Managorger Hydra no matter how many spells were cast this turn (note that the ability doesn't say "... for each spell cast this turn").