Praise be to Allah.
It was narrated that al-Nawwaas ibn Sam‘aan said: The Messenger of Allah (blessings and peace of Allah be upon him) mentioned the Dajjaal one morning, sometimes describing him as insignificant and sometimes describing him as significant…
Then whilst he [the Dajjaal] is like that, Allah will send the Messiah son of Maryam (peace be upon him), who will descend to the white minaret in the east of Damascus, wearing two garments lightly perfumed with saffron, placing his hands on the wings of two angels. When he lowers his head it will drip and when he raises it, it will scatter drops like pearls. Every disbeliever whom his breath reaches will die, and his breath will reach as far as he can see. He will pursue him until he catches him at the gate of Ludd (Lod), and kills him …
Narrated by Muslim (2937).
What Allah, may He be exalted) granted to ‘Eesa (peace be upon him) of the proofs of prophethood in the past, such as giving life to the dead, and what He will grant to him in the future, of the disbeliever dying by his breath, as mentioned in this hadith – all of that is nothing to be confused about. Rather Allah, may He be exalted, has granted him this as proof of the truthfulness of his message. People of sound reason and common sense will find in this proof of the sincerity and truthfulness of ‘Eesaa in his words and deeds. Hence these miracles are called signs of prophethood.
The confusion that you refer to in your question may be applicable if we assume that ‘Eesa (peace be upon him) was given these signs, but then kept quiet and did not explain the truth. Then the people might speculate about him and wonder about him, if he had kept silent and did not explain anything. But ‘Eesa (peace be upon him) was given these proofs when he was striving to do what Allah, may He be glorified, had commanded him to do of calling people to affirm the oneness of Allah, may He be exalted, and to declare Him above having any partner or son.
This is what he (peace be upon him) did in the past. Allah, may He be exalted, says (interpretation of the meaning):
“And [make him] a messenger to the Children of Israel, [who will say], ‘Indeed I have come to you with a sign from your Lord in that I design for you from clay [that which is] like the form of a bird, then I breathe into it and it becomes a bird by permission of Allah . And I cure the blind and the leper, and I give life to the dead - by permission of Allah . And I inform you of what you eat and what you store in your houses. Indeed in that is a sign for you, if you are believers.
‘And [I have come] confirming what was before me of the Torah and to make lawful for you some of what was forbidden to you. And I have come to you with a sign from your Lord, so fear Allah and obey me
‘Indeed, Allah is my Lord and your Lord, so worship Him. That is the straight path’”
[Aal ‘Imraan 3:49-51]
“And [beware the Day] when Allah will say, ‘O Jesus, Son of Mary, did you say to the people, “Take me and my mother as deities besides Allah ?”’ He will say, ‘Exalted are You! It was not for me to say that to which I have no right. If I had said it, You would have known it. You know what is within myself, and I do not know what is within Yourself. Indeed, it is You who is Knower of the unseen
‘I said not to them except what You commanded me - to worship Allah , my Lord and your Lord. And I was a witness over them as long as I was among them; but when You took me up, You were the Observer over them, and You are, over all things, Witness’”
This is what will happen when ‘Eesa (peace be upon him) descends at the end of time, to rule in accordance with Islamic law; he will not accept anything from the Christians except Islam, and he will not accept any jizyah. Some Christians will become Muslim, because the truth will become manifest and clear. This is very clear indeed, that there will be no confusion or misunderstanding at this time, for ‘Eesa (peace be upon him) is the Prophet of Allah and His Messenger. He will never call people at the end of time, when he descends, to his own laws; rather he will not accept for them to follow the religion of Christianity that they made up themselves, and whoever has been following Christianity at the time when he descends, it will not be acceptable for him to continue in it after the descent of ‘Eesa ibn Maryam (peace be upon him). So how could there be any fear of confusion in this case, or how can it be thought that there would remain any ambiguity or doubt?
It was narrated that Abu Hurayrah (may Allah be pleased with him) said: The Messenger of Allah (blessings and peace of Allah be upon him) said: “By the One in Whose hand is my soul, soon the son of Maryam will descend among you as a just judge. He will break the cross, kill the swine and waive the jizyah. Wealth will become so abundant that no one will accept it [as charity].” Narrated by al-Bukhaari (2222) and Muslim (155).
Ibn Katheer (may Allah be pleased with him said, after quoting this:
These hadiths are narrated from the Messenger of Allah (blessings and peace of Allah be upon him) in mutawaatir reports from Abu Hurayrah, Ibn Mas‘ood, ‘Uthmaan ibn Abi’l-‘Aas, Abu Umaamah, an-Nawwaas ibn Sam‘aan, ‘Abdullah ibn ‘Amr ibn al-‘Aas, Mujammi‘ ibn Jaariyah and Abu Sareehah Hudhayfah ibn Usayd (may Allah be pleased with them all).
This is indicative of how and where he will descend. Then he will kill the pigs, break the cross and abolish the jizyah, and he will not accept anything except Islam, as noted above in al-Saheehayn. This is foretelling on the part of the Prophet (blessings and peace of Allah be upon him) of this, approving of it and allowing it, thus paving the way for what will happen at this time, as they will have no more excuses and there will be no reason for any doubts. Hence all of them will enter the religion of Islam, following ‘Eesa (peace be upon him) and at his hands. Hence Allah, may He be exalted, says (interpretation of the meaning):
“And there is none from the People of the Scripture but that he will surely believe in Jesus before his death. And on the Day of Resurrection he will be against them a witness”
This is like the verse in which Allah, may He be exalted, says (interpretation of the meaning):
“And indeed, Jesus will be [a sign for] knowledge of the Hour”
The word ‘ilm, translated above as knowledge, may also be read as ‘alam, meaning a sign and indication that the Hour is at hand.
End quote from Tafseer Ibn Katheer (2/464-465).
So the descent of ‘Eesa (peace be upon him) at that time will remove any doubts in the minds of those who took him as a god.
And Allah knows best.