The stock of karma has the kleśas as its root. It is experienced in present or future lives.

Bryant Commentary:

Vyāsa states that the deposit, or stock of karma mentioned by Patañjali here, the karma-āsaya, is produced from kāma, lobha, moha, and krodha: desire, greed, delusion, and anger. Vyāsaappears to be using a variant set of terms overlapping the kleśas, perhaps taken from the Gītā (for example, XVI.21). Desire and its uncontrolled form of greed are ultimately the kleśas of attachment, and its flip side, aversion (which stem from the kleśas of ego and ignorance); anger is the frustration of this desire or attachment (Gītā II.62–63); and delusion is a manifestation of the kleśa of ignorance.

Vyāsa then discusses varieties of karma, good and bad, and its fructification. The examples Vyāsa gives of good karma include performing austerities, chanting mantras, cultivating samādhi, and worshipping Īśvara or the great sages, with enthusiasm and determination. Such activities bear fruit in this lifetime. He illustrates bad karma as harmful activities directed against the fearful, infirm, or helpless; those who have placed faith in oneself; the noble minded; or those performing austerities. If these activities are performed intensely, they can bear their fruits during the present life. Vyāsa illustrates the instant fructification of good karma by referring to the youth Nandīśvara, whose human form was transformed into a celestial one in that very life due to his intense performance of pious activities. He illustrates the immediate fructification of bad karma by the story of Nahuṣa, who was cursed by a sage to immediately abandon his celestial form as Indra and assume the form of a snake in the earthly realms due to his arrogance. Neither of these individuals had to undergo the normal process of old age and death but experienced their just fruits instantly. Similarly, the Bhāgavata (X.10) tells the story of two celestials who were cursed to become trees in the courtyard of Kṛṣṇa’s family home due to offending sage Nārada with their shameless licentious behavior. Baby Kṛṣṇa pulls down the two trees by dragging a mortar behind him that becomes wedged between them, and the two celestials are immediately released from their curse and regain their celestial forms.

Whether good or bad, all karma is stored or imprinted as saṁskāra in the citta and, in general, may manifest its fruits in either this life or the next. Activities are virtuous or nonvirtuous and produce corresponding fruits. In the next sūtra, Patañjali states that the particulars of one’s life—the type of birth, quality of life experience, and life span—are all the fruits or results of one’s karma. But the fruits of karma ultimately have the kleśas as their root, mūla; it is these kleśas that influence one to act in good or bad ways. Therefore, there is a vicious cycle: kleśas provokes karma, and karma fuels the kleśas.

Vācaspati Miśra gives a few examples of how the desire, greed, delusion, and anger noted by Vyāsa might produce either bad or good karma. Desire can obviously produce bad karma when one performs impious acts out of avarice, such as stealing another person’s property, but desire can also produce good karma, as when one performs pious acts motivated by a desire to enjoy the rewards of piety. Bad karma caused by anger, says Vācaspati Miśra, hardly needs exemplification—murder of the righteous, etc.—but there are also instances when anger produces good karma. Here he refers to the famous Purānic story of prince Dhruva, a child devotee of Viṣṇu (Bhāgavata Purāṇa IV.9–12ff). Once, Dhruva attempted to climb onto his father’s lap but was rebuked by his co-mother, who wanted her own son, Dhruva’s half brother, to be the king’s favorite and eventual successor to the throne. Offended that his father did not step in when he was humiliated in this way, Dhruva determined in anger to gain a kingdom greater than his father’s. Upon asking his own mother to advise him as to who might help him achieve his ends, she told him that he should worship Viṣṇu, since Viṣṇu can bestow any boon. Even though the boy was only five years old, and even though the great sage Nārada tried to dissuade him on account of the perils and hardships of the forest where he was heading, the boy persisted and performed intense austerities with his mind fixed on Viṣṇu. Eventually, as a result of concentrating his mind so exclusively on the supreme Lord in this way, Viṣṇu appeared to him and Dhruva was purified and received immeasurable boons, both material and spiritual. The point is that even though Dhruva worshipped Viṣṇu out of anger at the offense he had suffered, his mind was completely fixed without deviation on Īśvara and from this perspective created good karma (although a vision of Viṣṇu is, of course, an act of grace and beyond the jurisdiction of any mundane laws of karma).

A verse in the Bhāgavata Purāṇa states that “those who always dedicate their desire, anger, fear, affection, sense of identity, and friendship to Hari [Kṛṣṇa], enter for certain into his state of being” (X.29.15). According to the Bhāgavata, the highest meditation and goal of life is total absorption in God, even if this is generated out of animosity, as was the case with Kaṁsa, who, along with other demoniac adversaries of Kṛṣṇa, attained liberation simply by virtue of their minds being fixed undeviatingly on God, albeit in animosity. The text states: “The king of the Cedis, Śiśupāla, attained perfection despite hating Kṛṣṇa; what then of those dear to him?!” (X.29.13). The bottom line for the Bhāgavata is a samādhi with the mind fixed exclusively on Kṛṣṇa as Īśvara, whether in anger and hatred, or in a mood of intense desire and love, as with the gopī cowherd-women—all qualities which, under any other circumstances, would be considered kleśas.

Returning to Vyāsa’s list, delusion can generate bad karma, as in the case of taking the life of another under the belief that doing so is a virtuous act, but delusion, according to Vācaspati Miśra does not beget good karma. However, even here, one might think of instances where delusion provokes a positive outcome in Purāṇic narratives. Bali, the king of the demons, for example, was deluded by Viṣṇu who appeared before him in the form of a brāhman˙a boy Vāmana, and tricked him out of his lordship of the three worlds. Yet the episode ends in Bali’s upliftment (see IV.2 for story) since he attained pure devotion to Viṣṇu (Īśvara).24

Vijñānabhikṣu notes that the laws of karma apply only when they are performed out of ego, when they are performed out of ego, which, we recall, Patañjali defines as confounding the true puruṣa self with the mind and body. He quotes the Gītā, where Kṛṣṇa is encouraging the despondent warrior Arjuna to fight a righteous war out of a sense of duty rather than out of concern for the outcome that might result for him personally: “One whose intelligence is not tainted by ego, though he kills people in this world, does not kill, nor is he bound by his actions” (XVIII.17).
Hariharānanda provides the following useful synopsis of the workings of karma: Any state of mind leaves an imprint of itself on the citta, and, as we know, this imprint is called a saṁskāra. Imprints of good and bad karma produce an accumulation of saṁskāras called the karmāśaya, or stock of karma (II.12). These saṁskāras are either born from the kleśas, or are not: Those produced out of ignorance are born from the kleśas, but those resulting from true understanding are not (such as the “terminator” saṁskāra of I.50). It is the former category of saṁskāras born from the kleśas, whether pious, impious, or mixed in nature, that produces the store of karma, the karmāśaya. This store of karma then fructifies and brings about the threefold conditions of one’s life that are the subject of the next sūtra. The time it takes for the seeds of karma to fructify—whether in this life or a future one—depends on the intensity of the original saṁskāra.

Avidya Is The Breeding Ground For The Others Whether They Be Dormant, Attenuated, Interrupted Or Active

The causes of suffering are not seeing things as they are, the sense of ‘I’, attachment, aversion, and clinging to life.

Ignorance is the fertile soil,
and, as a consequence,
all other obstacles persist.
They may exist in any state – dormant, feeble, intermittent,
or fully operative.

The lack of awareness of Reality, the sense of egoism or ‘I-am-ness’, attractions and repulsions towards objects and the strong desire for life are the great afflictions or causes of all miseries in life.

The five afflictions which disturb the equilibrium of consciousness are: ignorance or lack of wisdom, ego, pride of the ego or the sense of ‘I’, attachment to pleasure, aversion to pain, fear of death and clinging to life.

Ignorance, egoism, attachment, hatred, and clinging to bodily life are the five obstacles.

The root being there, the fruition comes (in the form of) species, life, and expression of pleasure and pain.

SV Commentary:

The roots, the causes, the Samskaras being there, they again manifest, and form the effects. The cause dying down becomes the effect, and the effect becomes more subtle, and becomes the cause of the next effect. The tree bears a seed, and becomes the cause of the next tree, and so on. All our works now, are the effects of past Samskaras. Again, these Samskaras become the cause of future actions, and thus we go on. So this aphorism says that the cause being there, the fruit must come, in the form of species; one will be a man, another an angel, another an animal, another a demon. Then there are different effects in life; one man lives fifty years, another a hundred, and another dies in two years, and never attains maturity; all these differences in life are regulated by these past actions. One man is born, as it were, for pleasure; if he buries himself in a forest pleasure will follow him there. Another man, wherever he goes, pain follows him, everything becomes painful. It is all the result of their own past. According to the philosophy of the Yogis all virtuous actions bring pleasure, and all vicious actions bring pain. Any man who does wicked deeds is sure to reap the fruit of them in the form of pain. 

Here the vehicle of good and bad actions is born of lust, avarice, forgetfulness and anger. Its operation is felt in the visible as well as in the invisible birth. Of these, the vehicle of good actions, which is supplemented by intense energy in the shape of purificatory action, meditation and repetition of mantras, or, which is accompanied by devotion to the Lord, the devas, the great seers and other possessors of great power, ripens into fruit at once. This happens in the same way in which, in the event of repeated evil done to men who are suffering the extreme misery of fear, disease and helplessness, or to those who place confidence in the evil-doer, or to those who are high-minded and perform tapas , the vehicle of evil-actions also ripens into fruit at once. As for example, the youth Nandishwara passed out of the human form and was transformed into a god. As also Naliusa, the ruler of the gods, passed out of his own form and was transformed into an animal. Of the vehicles of action, that which culminates into the life of hell, is said to be experienced in the invisible birth.

As to those whose afflictions have been destroyed, the vehicle of actions is not experienced in the invisible births.

~ Rāma Prasāda translation.