Can God act against His will?

First the whole verse to get the flow of it:

"The Lord is not slow to fulfill his promise as some count slowness, but is patient toward you, not wishing that any should perish, but that all should reach repentance." 2 Peter 3:9 ESV

A. "patient towards you". 2 Peter 3:1 "I am writing to you, beloved", "you" are "beloved".

See 2 Peter 1:1 The letter is addressed to "those who have obtained a faith" i.e. Christians.

B. "not wishing that any". "any" who? Any in the church to whom the letter is addressed. [Not any in the world. The world is not mentioned here].

C. "but that all", all in the church. God is patient towards Christians as they mess up again and again but God does not wish that those in Christ perish, but that they repent- go to confession, confess to each other, confess to God, whatever is relevant to their level of sin, and situation.

Repentance is not a once event: "But if anyone does sin, we have an advocate with the Father, Jesus Christ the righteous." 1 John 2:1 "anyone" may sin; anyone here is addressed to "My little children".

"My little children" are those who are taking advantage of "we have an advocate with the Father". Others may have or not have heard of Jesus, but the children are walking in the light of that truth. They are the ones who "know that we have come to know him" 1 John 2:3.

2 Timothy 2:13 (ASV) if we are faithless, he abideth faithful; for he cannot deny himself.

God cannot deny Himself - which means He carries out the mandates of His will always. However, there seems to be a hierarchy of precedence, the highest of which is the inviolability of the will of all His created beings. God has chosen to never force anyone and He remains true to this principle which tops the list - this is His will, an everlasting mandate. When our will clashes with God's will, in matters which are under our control - like our choice to be saved, God does not interfere. Though the loss of each soul weighs heavily upon Him.

Firstly, it's unclear whether your are asking about God's volition or about His desire. Both are fair questions, and since jaredad7 already responded to the one, I'll start instead by looking at the verse you mentioned:

The Lord [...] is longsuffering toward us, not willing that any should perish (NKJV)

(Original KJV differs only in using the split preposition "to us-ward".)

However, if you compare other translations, most use "wish[ing]", and a few use "wanting". It seems clear that the original word indicated desire rather than volition, which breaks your premise, at least as following from the originally cited verse. Moreover, if we check the interlinear, the original Greek βουλόμενός is also consistent with an expression of preference.

That's not to say KJV is "wrong", per se, as "to wish or desire" is a recorded historic meaning for the verb "will" (n.b. definitions 6 and 7); indeed, the aforementioned BH interlinear lists "to will" as one of the translations of βουλόμενός (along with "to wish" and "to desire"). Unfortunately, such usage here is ambiguous, particularly to modern readers, which is likely why newer translations use a different word.

So... now that we're looking at the question of God acting against His desire... can He do that?

Well... it would be easy to say "yes", just as I might desire to eat another scoop of ice cream, but am able to resist. The issue at play here is that there is conflict; on the one hand, ice cream is tasty, but on the other it's unhealthy. Condemning unrepentant sinners is Just, even if God would prefer to not condemn anyone.

No, God cannot act against His own will, as that would be a contradiction. No one can act against his own will, though one can allow things that one does not will to pass by refraining from action. That is what God does. Though He does not will that any perish, He also does not force all to accept His grace and be saved.