First, science does not say that atoms, matter, is indestructible. There wouldn't be any atomic bombs if it were.
There is a general answer and a detailed answer as to what does scripture say. Krishna says in Gita Chapter 8, verses 18 and 19 (Swami Gambhirananda translator):
Now cosmic dissolution is being described. It is the destruction of the world in general. It is of four kinds—diurnal, basic, occasional and absolute. Of these, diurnal (nitya) dissolution is the condition of profound sleep, for it represents the dissolution of all effects. Merit, demerit and past latent impressions then remain in their causal form. Hence, for a person awaking from sleep, pleasure, pain, etc. are not incongruous; nor is recollection inexplicable. Though the mind is destroyed in profound sleep, yet the function of respiration etc., which depend on that, are not incongruous, because, although in reality there are no respiration etc., yet their knowledge is just a phantasy of another person,’ like the knowledge of the body of a sleeping man.* It cannot be urged that in that case a sleeping man would be indistinguishable from a dead man; for there is this distinction that the subtle body of a sleeping man remains here itself in the form of latent impressions, while that of a dead man remains in another world.
Or* the mind has two functions—the function of knowledge and that of activity. Of these, the mind as possessed of the function of knowledge is destroyed in profound sleep, but not the mind as possessed of the function of activity. Hence the continuity of the vital force etc. is not contradictory. Sruti texts like the following are proofs of the above condition of profound sleep: * When a person is asleep and sees no dreams, he verily becomes one with (Brahman associated with) this vital force. Then the organ of speech with all names merge in It" (Kau. IV. 19), “He is then united with Existence, my dear—is merged in his Self” (Cha. VI. viii. 1). [* To explain it differently.]
Basic dissolution is the destruction of all effects consequent on the destruction of Hiranyagarbha. (To be explicit:) When Hiranyagarbha, who has already' had realisation of Brahman, attains, on the termination of his fructifying (prarabdha)* work in the form of suzerainty of the universe, supreme liberation consisting in isolation characterised by disembodiedness, then those denizens of the world® of Hiranyagarbha who* have already realised Brahman, also attain with him isolation characterised by disembodiedness. Witness the Smrti text, ‘“ When, at the end of the lifetime of Hiranyagarbha, cosmic dissolution comes, all those who have realised the Self enter the supreme state with him’ (Ku. I. xii. 269). Thus, when Hiranyagarbha together with the inhabitants of his world is liberated, the universe ruled by him, with all its subsidiary worlds® and the stationary® or other bodies, made up of the elements, that are comprised in them, as also those elements themselves, is merged in prakrti or the cosmic illusion (maya), and not in Brahman—for only destruction in the form of nullification (badha)’ abides in Brahman.®* Therefore it is called basic (prakrta).®
[* Before the dissolution of the universe.
2Lit., ‘commenced’: that is, that part of one’s past work which has already begun to bear fruit by causing the present body. It is exhausted through actual experience of pleasure and pain.
“Not others who have gone there through the mechanical performance of certain rites.
The fourteen worlds enumerated on p. 170.
Such as those of plants.
See p. 63.
® As its substratum. See p. 75.
®Lit., ‘pertaining to praksti’ or the primal material cause of the universe.]
The dissolution of only three’ worlds consequent on the end of a day of Hiranyagarbha is occasional dissolution. A day of Hiranyagarbha is a period measured by four thousand eras (yuga),* as we have it from such scriptural statements as, ‘‘A period of four thousand eras is called a day of Brahma’ (Brhannar. XXXII. 86). The period of dissolution also is as long as the day, for the duration of a night is equal to that of a day.
[* The earth, sky and heaven. 2 Equivalent to 4,320,000 human years.]
Regarding basic and occasional dissolution, the statements of the Puranas are proofs. The statement, ‘“ When two hundred thousand billion human years comprising the lifetime of Hiranyagarbha, the Paramesthin, have passed, the seven causes’ undergo dissolution.” This, O King, is basic dissolution, when (every effect) is merged,” is a proof of basic dissolution. And the statement, ‘“That is called occasional dissolution when the Creator® of the universe regularly* withdraws the three worlds into himself, and lies’ on the serpent Ananta as his bed,’” is a proof of occasional dissolution.
[* Entities that are causes only and never effects, viz., the cosmic mind, the ego and the five subtle elements.
*In the primal praksti.
2 Brahma or Hiranyagarbha.
4On the approach of every night of his.
$ As identified with Visnu.]
The fourth kind of dissolution is the liberation of all' consequent on the realisation of Brahman. According to the doctrine of a single individual self,? it is just simultaneous, but according to the doctrine of multiple individual selves,® it is gradual. Witness Sruti texts like, “All are united.”
Of the above kinds of dissolution the first three* are all caused by the cessation® of past work,® while the fourth kind of dissolution is due to the dawning of knowledge, and it takes place together with the dissolution of nescience itself. This is its difference from the others.
[* In which there is a destruction of all created things together with their cause, nescience.
2In. which nescience, which is one, is the limiting adjunct of the self.
3In which the different minds are the limiting adjuncts. ’
4Viz., diurnal, basic and occasional.
Due to one’s profound sleep, the passing of Hiranyagarbha, and his falling asleep respectively.
¢ Of individuals ; but not the cessation of nescience.]
The Order of Cosmic Dissolution
Thus the four kinds of cosmic dissolution have been described. Now the order of such dissolution is being set forth. The dissolution of the elements and of things made out of them is not according to the order of the dissolution of their causes—for when the causes are dissolved, the effects cannot possibly stay without substratums —but it is in the inverse order to that of projection. For with regard to the destruction of particular effects, the destruction of the particular merits or demerits that caused them is the sole determining factor; hence the destruction of their material causes is not a necessary condition. Otherwise, even according to Nyaya, the colour, taste, etc., belonging to atoms of earth would not be destroyed’ at cosmic dissolution. So dis- solution takes place in the following manner: Earth is merged in water, water in fire, fire in air, air in the ether, the ether in the ego® of the individual self, that in the ego of Hiranyagarbha, that, again, in nescience. So it has been said in the Visnu Purana,’ ‘ Earth, which is the support of the world, O divine sage (Narada), is merged in water, water is merged in fire, fire in air, and air in the ether; this in its turn is merged in the Undifferentiated, and the Undifferentiated, O Brahman, in the Supreme Self, which is devoid of parts.”
The secondary characteristic’ of Brahman, the meaning of the word ‘That,’ is that It is the cause of this kind of dissolution.
[ Since, according to Nyaya, atoms are eternal.
2 That is, the subtle body.
3 The passage does not seem to occur in the available editions of the book.
See p. 81.
¢In the dictum, ‘Thou art That.”’]
And in agreement with this, the next two verses following the above quoted verses of the Gita say (8.20 and 21):