Bismillah,

Allah Taala said in His Book:

[Shakir 9:40] If you will not aid him, Allah certainly aided him when those who disbelieved expelled him, he being the second of the two, when they were both in the cave, when he said to his companion: Grieve not, surely Allah is with us. So Allah sent down His tranquillity upon him and strengthened him with hosts which you did not see, and made lowest the word of those who disbelieved; and the word of Allah, that is the highest; and Allah is Mighty, Wise.

This verse tells us story of migration, which was perfectly told by allama al-Mubarakfoore:

When the iniquitous decision had been made, Gabriel was sent down to Muhammad (Peace be upon him) to reveal to him Quraish’s plot and give him his Lord’s Permission to leave Makkah. He fixed to him the time of migration and asked him not to sleep that night in his usual bed. At noon, the Prophet (Peace be upon him) went to see his Companion Abu Bakr and arranged with him everything for the intended migration. Abu Bakr was surprised to see the Prophet (Peace be upon him) masked coming to visit him at that unusual time, but he soon learned that Allâh’s Command had arrived, and he proposed that they should migrate together, to which the Prophet (Peace be upon him) gave his consent.

To make the necessary preparations for the implementation of their devilish plan, the chiefs of Makkah had chosen eleven men: Abu Jahl, Hakam bin Abil Al-‘As, ‘Uqbah bin Abi Mu‘ait, An-Nadr bin Harith, Omaiyah bin Khalaf, Zama‘a bin Al-Aswad, Tu‘aima bin ‘Adi, Abu Lahab, Ubai bin Khalaf, Nabih bin Al-Hajjaj and his brother Munbih bin Al-Hajjaj. All were on the alert. As night advanced, they posted assassins around the Prophet’s house. Thus they kept vigil all night long, waiting to kill him the moment he left his house early in the morning, peeping now and then through a hole in the door to make sure that he was still lying in his bed. Abu Jahl, the great enemy of Islam, used to walk about haughtily and arrogantly jeering at Muhammad’s words, saying to the people around him: “Muhammad claims that if you follow him, he will appoint you rulers over the Arabs and non-Arabs and in the Hereafter your reward will be Gardens similar to those in Jordan, otherwise, he will slaughter you and after death you will be burnt in fire.” He was too confident of the success of his devilish plan. Allâh, the All-Mighty, however, in Whose Hands lie the sovereignty of the heavens and earth, does what He desires; He renders succour and can never be overpowered. He did exactly what He later said to His Prophet:

“And (remember) when the disbelievers plotted against you [O Muhammad (Peace be upon him)] to imprison you, or to kill you, or to get you out (from your home, i.e. Makkah); they were plotting and Allâh too was planning, and Allâh is the Best of the planners.” [8:30]

At that critical time the plans of Quraish utterly failed despite the tight siege they laid to the Prophet’s house, the Prophet (Peace be upon him) and ‘Ali were inside the house. The Prophet (Peace be upon him) told ‘Ali to sleep in his bed and cover himself with his green mantle and assured him full security under Allâh’s protection and told him that no harm would come to him. The Prophet (Peace be upon him) then came out of the room and cast a handful of dust at the assassins and managed to work his way through them reciting verses of the Noble Qur’ân:

“And We have put a barrier before them, and a barrier behind them, and We have covered them up, so that they cannot see.” [36:9]

He proceeded direct to the house of Abu Bakr who, immediately accompanied him and both set out southwards, clambered up the lofty peak of Mountain Thawr, and decided to take refuge in a cave.

The assassins who laid siege to the house were waiting for the zero hour when someone came and informed them that the Prophet (Peace be upon him) had already left. They rushed in and to their utter surprise, found that the person lying in the Prophet’s bed was ‘Ali not Muhammad (Peace be upon him). This created a stir in the whole town. The Prophet (Peace be upon him) had thus left his house on Safar 27th, the fourteenth year of Prophethood, i.e. 12/13 September 622 A.D.

Knowing already that Quraish would mobilize all its potentials to find him, he played a clever trick on them and instead of taking the road to Madinah in north side of Makkah as the polythiest would expect, he walked along a road least expected lying south of Makkah and leading to Yemen. He walked for 5 miles until he reached a rough rocky mountain called Thawr. There his shoes were worn out, some said he used to walk tiptoe in order not to leave a trail behind him. Abu Bakr (May Allah be pleased with him) carried him up the mountain to a cave called after the name of the mountain, Cave Thawr. Abu Bakr first entered to explore the cave and be sure that it was safe, closed all holes with pieces torn off from his clothes, cleaned it and then asked the Prophet (Peace be upon him) to step in. The Prophet (Peace be upon him) went in and immediately laid his head in Abu Bakr’s lap and fell asleep. Suddenly Abu Bakr’s foot was stung by a poisonous insect. It hurt so much that his tears fell on the Prophet’s face. The Prophet (Peace be upon him) immediately applied his saliva on Abu Bakr’s foot and the pain went off on the spot. They confined themselves to this cave for three nights, Friday, Saturday and Sunday. ‘Abdullah, the son of Abu Bakr would go to see them after dusk, stay the night there, apprise them of the latest situation in Makkah, and then leave in the early morning to mix with the Makkans as usual and not to draw the least attention to his clandestine activities. ‘Amir bin Fuhairah, while in the company of other shepherds of Makkah tending his master Abu Bakr’s flock, used to stole away unobserved every evening with a few goats to the cave and furnished its inmates with a plentiful supply of milk.

Quraish, on the other hand, were quite baffled and exasperated when the news of the escape of the two companions was confirmed. They brought ‘Ali to Al-Ka‘bah, beat him brutally and confined him there for an hour attempting desperately to make him divulge the secret of the disappearance of the two ‘fugitives’, but to no avail. They then went to see Asma’, Abu Bakr’s daughter, but here also their attempts went in vain. While at her door Abu Jahl slapped the girl so severely that her earring broke up.

The notables of Makkah convened an emergency session to determine the future course of action and explore all areas that could help arrest the two men. They decided to block all avenues leading out of Makkah and imposed heavy armed surveillance over all potential exits. A price of 100 camels was set upon the head of each one. Horsemen, infantry and tracers of tracks scoured the country. Once they even reached the mouth of the cave where the Prophet (Peace be upon him) and Abu Bakr were hiding. When he saw the enemy at a very close distance, Abu Bakr whispered to the Prophet (Peace be upon him): “What, if they were to look through the crevice and detect us?” The Prophet (Peace be upon him) in his God-inspired calm replied:

“Silence Abu Bakr! What do you think of those two with whom the Third is Allâh.”

It was really a Divine miracle, the chasers were only a few steps from the cave.

For three days Muhammad (Peace be upon him) and Abu Bakr lived in the cave and Quraish continued their frantic efforts to get hold of them.

The fact that Abu Bakr was with prophet (sallalahu alaihi wa ala alihi wa sallam) during his migration, and that it was him whom prophet (salallahu alaihi wa ala alihi wa sallam) addressed with words: Grieve not, surely Allah is with us, is something well established in the view of Islamic nation.

But surprisingly we have seen some shias rejecting this!

However we would like to bring them words of their scholar, Tabatabai, from his commentary.

He said:

والمراد بصاحبه هو أبو بكر للنقل القطعي

And the meaning of companion is Abu Bakr in accordance to concrete (qatiy) report

Abu Jafar at-Toose in his commentary “Tibyan” wrote:

وهو ابو بكر في وقت كونهما في الغار من حيث { قال لصاحبه } يعني ابا بكر { لا تحزن } اي لا تخف.

And that was Abu Bakr in the time when they were in the cave, when ( said to his companion) meaning Abu Bakr, (grieve not) meaning don’t be afraid

Other shia scholar and commentator Faydh al-Kashani in his “Safi” said:

إذْ يَقُولُ لِصَاحِبِهِ } وهو أبو بكر { لاَ تَحْزَنْ } لا تخف

When he said to his companion – that was Abu Bakr, grieve not – don’t be afraid.