In the battle between the Jews and the Muslims at the end of time, the aggressors will be the Jews

Praise
be to Allah

Firstly: 

Islam is the religion of mercy and peace, as the questioner
describes it. Therefore, Islam allowed the Jews and Christians to remain in
Muslim lands, and did not expel them or kill them, as they did and still do
when they gain control over Muslim lands. That is in accordance with the
treaty between them and the Islamic state, with both parties having rights
and duties. So long as they continue to adhere to those conditions, they
have the right to enjoy that right of residence and security. 

Hence Islam offers protection to ahl adh-dhimmah in Muslim
lands, and defends their rights if they adhere to the conditions of
residence, to the extent that the Prophet (blessings and peace of Allah be
upon him) said: “Whoever kills a mu‘ahid (non-Muslim living under Muslim
rule) will not smell the fragrance of Paradise, even though its fragrance
may be detected from a distance of forty years.” Narrated by al-Bukhari
(3166). 

And he (blessings and peace of Allah be upon him) said:
“Whoever wrongs a mu‘ahid, detracts from his rights, burdens him with more
work than he is able to do or takes something from him without his consent,
I will plead for him (the mu‘ahid) – or I will be the opponent of (the
Muslim who wronged him) – on the Day of Resurrection.”

Narrated by Abu Dawood (3052); classed as hasan by Ibn Hajar
in Muwafaqat al-Khabr (2/184); classed as saheeh by al-Albani in
Saheeh Abi Dawood. 

But if they break the conditions – such as if they commit
acts of betrayal or treachery, or they prepare to fight us or help our
enemies, and the like – then they have broken the treaty, and in that case
there is no treaty between us and them, and they do not deserve to reside in
security as they did not uphold the treaty.

Secondly: 

Yes, the Muslims used to coexist with the Jews and treat them
well, so long as they adhere to the conditions of residence. But they may
choose to be treacherous. It is sufficient for you to know that when the
Messenger (blessings and peace of Allah be upon him) migrated to Madinah,
there were three Jewish tribes in the city, namely Banu Qaynuqa‘, Banu an-Nadeer
and Banu Qurayzah. He made treaties with all of them and agreed to live in
peace with all of them, but they all committed acts of treachery and
betrayal. 

Therefore the Messenger (blessings and peace of Allah be upon
him) fought them, killing some of them and banishing others beyond Madinah,
and he did not allow them to remain in the city. 

Thirdly: 

Al-Bukhari (3593) and Muslim (2921) narrated from the hadith
of Ibn ‘Umar (may Allah be pleased with him) that he said: I heard the
Messenger of Allah (blessings and peace of Allah be upon him) say: “The Jews
will fight you and you will prevail over them, then a rock will say: ‘O
Muslim, here is a Jew behind me; kill him.’” 

In Saheeh Muslim (2922), it is narrated from the
hadith of Abu Hurayrah that the Messenger of Allah (blessings and peace of
Allah be upon him) said:
“The Hour will not begin until the Muslims fight the Jews and the Muslims
will kill them, until a Jew hides behind a rock or a tree, and the rock or
tree will say: O Muslim, O slave of Allah, there is a Jew behind me, come
and kill him. Except the gharqad (a thorny tree), for it is one of
the trees of the Jews.” 

In some reports there is an indication that the fighting
against the Jews that is mentioned in this hadith will occur at the end of
time, when the Dajjal emerges and the Messiah ‘Eesa ibn Maryam (peace be
upon him) descends and fights him. 

‘Abdullah ibn ‘Umar (may Allah be pleased with him) narrated
that the Messenger of Allah (blessings and peace of Allah be upon him) said:
“The Dajjal will camp in this salty, barren ground in Marr Qanat [a valley
in Madinah], and most of those who go out to him will be women, to the
extent that a man will go back to his relative, to his mother, his daughter,
his sister and his paternal aunt, and will tie her up for fear that she may
go out to him. Then Allah will give the Muslims power over him, and they
will kill him and his party, until a Jew will hide beneath a tree or a rock,
and the rock or tree will say to the Muslim: ‘Here is a Jew beneath me; kill
him.’” 

Narrated by Imam Ahmad in al-Musnad (9/255). But there
is some weakness in its isnad because of the ‘an‘anah of Muhammad ibn Is-haq
[i.e., narration by saying ‘an (from) rather than saying So and so said/told
us].  There are other corroborating reports; see the commentary on al-Musnad
in the Mu’sasat ar-Risalah edition. 

These corroborating reports were quoted by al-Hafiz Ibn
Hajar (may Allah have mercy on him) in Fath al-Bari (6/610); he
classed as hasan the hadith of Samurah ibn Jundub (may Allah be pleased with
him), then he said: What is meant by fighting the Jews is that this will
happen when the Dajjal emerges and ‘Eesa descends. End quote. 

Ibn al-Mulqin said: What is meant by the words “You will
fight the Jews” is that this will happen when ‘Eesa descends; the Muslims
will be with him and the Jews will be with the Dajjal.

End quote from at-Tawdeeh li Sharh al-Jami‘ as-Saheeh
(17/663). 

This is what was stated definitively by a number of
commentators on the hadith. In fact Imam at-Tirmidhi (2236) narrated the
hadith of ‘Abdullah ibn ‘Umar, which is quoted above, in the chapter
entitled The Signs of the Dajjal (‘Alamaat ad-Dajjal). 

Shaykh al-Islam Ibn Taymiyah (may Allah have mercy on him)
said:

The Jews are in fact awaiting the false messiah (al-maseeh
ad-dajjal), for he is the one whom the Jews will follow. Seventy thousand
of the Jews of Isfahan wearing tayalisah (a kind of head covering) will
emerge with him. The Muslims will fight them with him, to the extent that
trees and rocks will say: “O Muslim, here is a Jew behind me; come and kill
him.”

End quote from al-Jawab as-Saheeh li man baddala Deen al-Maseeh
(2/30). 

Ash-Shaykh Ibn Baz (may Allah have mercy on him) said: 

‘Eesa (blessings and peace of Allah be upon him) will fight
him, supported by the Muslims, and he will kill him at the gate of al-Ludd (Lod),
which is in Palestine, near al-Quds (Jerusalem). He will kill him with his
spear, as it says in the saheeh hadith, and the Muslims who are with him
will kill a great number of the Jews. It says in the hadith from the Prophet
(blessings and peace of Allah be upon him) that the Muslims will fight the
Jews, and will kill them and gain power over them, and trees and rocks will
call out: O Muslim, O slave of Allah, here is a Jew; come and kill him. And
‘Eesa will kill the Dajjal and put an end to him. 

End quote from Fatawa Noor ‘ala ad-Darb by Ibn Baz,
ed by ash-Shuway‘ir (4/290) 

When the Dajjal emerges, thousands of the Jews will follow
him and rally around him, aiming to fight the Muslims. Then the Messiah
‘Eesa ibn Maryam (peace be upon him) will descend and the Muslims will rally
around him to fight the Dajjal and his followers. ‘Eesa ibn Maryam will
call the Jews to Islam, and he will not accept anything from them at that
time except Islam. Some of them will become Muslim and some of them will
remain followers of Judaism, then will come the battle that the Prophet
(blessings and peace of Allah be upon him) mentioned. 

Thus it is clear that the battle, for the Muslims, will be a
just and legitimate battle that Allah, may He be exalted, undoubtedly
approves of. This is indicated by the following: 

·       
It will be against the
Dajjal and his supporters who gathered to fight the Muslims.
“They
(the disbelievers, the Jews and the Christians) want to extinguish Allah’s
Light (with which Muhammad (blessings and peace of Allah be upon him) has
been sent – Islamic Monotheism) with their mouths, but Allah will not allow
except that His Light should be perfected even though the Kafiroon
(disbelievers) hate (it)”
[at-Tawbah 9:32].

·       
It will be a battle fought
by the Muslims under the leadership of ‘Eesa ibn Maryam (peace be upon him),
one of the noble Messengers.  

·       
Allah, may He be exalted,
will honour the Muslims in this battle with this miracle, which is that
rocks and trees will speak and call the Muslims to come and kill the Jews
who will be hiding behind them. 

All of this indicates that it will be a just battle that
Allah approves of, as was the case with all the Islamic battles in which the
aim was to make the word of Allah supreme on earth. “Whoever fights so that
the word of Allah will be supreme is fighting in the way of Allah.” Narrated
by Muslim (1915). 

And Allah knows best.