Although the Ninja is attacking, it was never declared as an attacking creature (for purposes of abilities that trigger whenever a creature attacks, for example).

If a creature in combat has first strike or double strike, you can activate the ninjutsu ability during the first-strike combat damage step. The Ninja will deal combat damage during the regular combat damage step, even if it has first strike.

The ninjutsu ability can be activated only after blockers have been declared. Before then, attacking creatures are neither blocked nor unblocked.

The token won’t copy counters, Auras, or Equipment on Mist-Syndicate Naga, nor will it copy other effects that have changed its power, toughness, types, color, or so on. Normally, this means the token will simply be a Mist-Syndicate Naga. But if any copy effects have affected Mist-Syndicate Naga, they’re taken into account.

The token will have Mist-Syndicate Naga’s ability. It will also be able to create copies of itself.

The ninjutsu ability can be activated during the declare blockers step, combat damage step, or end of combat step. If you wait until after the declare blockers step, because all combat damage is dealt at once, the Ninja won’t normally deal combat damage.

As you activate a ninjutsu ability, you reveal the Ninja card in your hand and return the attacking creature. The Ninja isn’t put onto the battlefield until the ability resolves. If it leaves your hand before then, it won’t enter the battlefield at all.

The creature with ninjutsu enters the battlefield attacking the same player or planeswalker that the returned creature was attacking. This is a rule specific to ninjutsu; in other cases, when a creature is put onto the battlefield attacking, that creature’s controller chooses which player or planeswalker it’s attacking.

If Mist-Syndicate Naga leaves the battlefield before its triggered ability resolves, the token will still enter the battlefield as a copy of Mist-Syndicate Naga, using Mist-Syndicate Naga’s copiable values from when it was last on the battlefield.