The Sahabah radiya Llahu ‘anhum understood the great loss and harm which the Muslims suffered in this battle to be destructive to the din of Islam. According to a report in Bukhari and Muslim, Sahl ibn Hunayf radiya Llahu ‘anhu, one of ‘Ali’s governors, remarked upon returning: “O people! Look at your opinions with eyes of suspicion (i.e. do not regard this slaying of Muslims as an act of reward). I had seen Abu Jandal (in chains) on the occasion of Hudaybiyyah. If there was a time when I was close to disobeying the command of Rasulullah salla Llahu ‘alayhi wa sallam it was only then (but I did not). I swear by Allah! Since we embraced Islam, we always felt no difficulty lifting our swords, except in this battle. We tried to seal a hole on one end but another opened on the other. We did not know how to remedy the situation.”
Sayyidina Rasulullah salla Llahu ‘alayhi wa sallam praised the stance of ‘Ali radiya Llahu ‘anhu, which he would take in the Battle of Nahrawan, saying:
يقاتلهم أولاهم بالحق
The one who is closer to the truth will fight the Khawarij.
(The Khawarij refers to those who disbanded from ‘Ali radiya Llahu ‘anhu and then attacked him. They comprised of the same rebels and murderers of ‘Uthman radiya Llahu ‘anhu from Egypt and Iraq) It should be borne in mind that there is no narration from Sayyidina Rasulullah salla Llahu ‘alayhi wa sallam praising any side of those who participated in the Battles of Jamal and Siffin. In fact, all the muhaddithin report these incidents under the chapters of fitan (trials and tribulations).
Undoubtedly, those who totally refrained from joining the battles were praised in abundance, such as Muhammad ibn Maslamah. It is narrated: “Two large groups of the Muslims will fight each other. Their claim will be the same (implementing the law of Allah). The one standing will be better than the one walking, and the one sitting will be better than the one who is standing. (i.e. to abstain from killing a Muslim is the greatest virtue.)”
Sayyidina Rasulullah salla Llahu ‘alayhi wa sallam also praised his grandson, Hassan radiya Llahu ‘anhu, saying: “He is a sayed (leader) whom Allah will use to bring together two large groups of the Muslims.” It is for this reason that Sayyidina Rasulullah salla Llahu ‘alayhi wa sallam once seated Hassan radiya Llahu ‘anhu together with Usamah ibn Zaid radiya Llahu ‘anhuma on his lap and said: “O Allah! I love them. You also love them and love those who love (follow) them.”
Usamah radiya Llahu ‘anhu said: “If you wish, you can throw me to the lions, but I will never lift my sword against a Muslim.”
The major problem which ‘Ali radiya Llahu ‘anhu faced was the rebels who had concealed themselves in his army. These were the real hypocrites and his true enemies. They left no stone unturned in spreading anarchy and keeping the Khalifah occupied with internal strife instead of allowing him to turn his attention to borders and furthering the successes of his predecessors. This was the ultimate objective of the hypocrites; to halt the forward march of the Muslims and forced them to consume themselves through civil war. However, ‘Ali radiya Llahu ‘anhu soon saw through the charade, albeit after these two Battles had been fought, and realised who his true enemies were. They were the very ones who were all along posing as his aids and assistants. It was the same rebels who murdered ‘Uthman radiya Llahu ‘anhu. It was then that ‘Ali radiya Llahu ‘anhu began cursing them repeatedly: “May you never be guided.”, “May you never be shown the straight path.”, “If only I had never met you and distanced myself from you”, “As long as the northerly and southerly winds blow, I will never call for you again.”
Nahj al Balaghah, the general history books and the books of the Shia as well, lament over the fact that every step taken by ‘Ali radiya Llahu ‘anhu had an adverse effect and resulted in more harm coming about, such that all the lands under his control began to slip away, one by one. The true cause of this is now apparent to you, it was the work of the ‘dark moles’ from within.
In order to remove a great administrator and tactician such as Qais ibn Sa’d ibn ‘Ubadah from his post, the rebels used their tried and tested plan; carrying tales to Egypt, Hijaz and on to Yemen. ‘Ali’s great assistant, his cousin ‘Abdullah ibn ‘Abbas radiya Llahu ‘anhu, was dismissed from his post as the governor of Basrah. ‘Ali’s elder brother, ‘Aqil ibn Abi Talib radiya Llahu ‘anhu was accused of making unlawful requests from the public treasury, and this subsequently sent him to Muawiyah radiya Llahu ‘anhu. The purpose behind these conspiracies was to remove the trustworthy from the inner circle of ‘Ali radiya Llahu ‘anhu. Since it was on the insistence of these sincere followers that ‘Ali radiya Llahu ‘anhu accepted the arbitration. It was then that the Khawarij separated from his army, and his own ‘followers’ chose to fight him instead.
Nevertheless, ‘Ali radiya Llahu ‘anhu fought against these Khawarij in the Battle of Nahrawan and defeated them. This is the battle which was praised by Rasulullah salla Llahu ‘alayhi wa sallam (as had been quoted earlier). Jafar Hussain (a Shia scholar), commenting on ‘Ali not gaining victory in Siffin, and attacked the faith and actions of the army of ‘Ali in the following words:
(No. 3 and 4 are blatant lies. If this was the case, they would have met with Muawiyah radiya Llahu ‘anhu before.)
These are the Saba’iyyah rebels who murdered ‘Uthman, Talhah and Zubair radiya Llahu ‘anhum. Now they wished to kill ‘Ali radiya Llahu ‘anhu as well. Why is it so farfetched to be accept that they are the same ones who killed ‘Ammar radiya Llahu ‘anhu?
When this Shia scholar, for his own benefit, is willing to tarnish the reputation of his own people in this manner, and regards it to be the height of scholastic scrutiny; then why is it regarded as indecorous to prove the enemies of these Sahabah to be evil and the most depraved of society?
 Bukhari vol. 2 pg. 602
 Bukhari and Muslim
 Nahj al Balaghah sermon: 117
 Nahj al Balaghah – urdu translation pg. 584