Firstly, this is an incorrect translation of this verse and the lack of mentioning the the entire verse and its context is highly suspicious. The word that is being misinterpreted by the questioner (or possibly the translation that was used) in Arabic is makara, which means to plan or to plot.
Secondly, the verse, in its proper context, is explaining that when the disbelievers plotted and planned against Jesus (peace be upon him) and his followers, that God (Allah) also had a plan and that He is the Best of those who plan. Below is the verse in question along with its proper context, taken from "The Noble Qur'an" translated by Hilali & Khan:
45. (Remember) when the angels said: "O Maryam (Mary)! Verily, Allah gives you the glad tidings of a Word ("Be!" - and he was! i.e. Iesa (Jesus) the son of Maryam (Mary)) from Him, his name will be the Messiah Iesa (Jesus), the son of Maryam (Mary), held in honour in this world and in the Hereafter, and will be one of those who are near to Allah."
46. "He will speak to the people in the cradle and in manhood, and he will be one of the righteous."
47. She said: "O my Lord! How shall I have a son when no man has touched me." He said: "So (it will be) for Allah creates what He wills. When He has decreed something, He says to it only: "Be!" and it is.
48. And He (Allah) will teach him (Iesa (Jesus)) the Book and Al-Hikmah (i.e. the Sunnah, the faultless speech of the Prophets, wisdom, etc.), (and) the Taurat (Torah) and the Injeel (Gospel).
49. And will make him (Iesa (Jesus)) a Messenger to the Children of Israel (saying): "I have come to you with a sign from your Lord, that I design for you out of clay, as it were, the figure of a bird, and breathe into it, and it becomes a bird by Allahs Leave; and I heal him who was born blind, and the leper, and I bring the dead to life by Allahs Leave. And I inform you of what you eat, and what you store in
your houses. Surely, therein is a sign for you, if you believe.
50. And I have come confirming that which was before me of the Taurat (Torah), and to make lawful to you part of what was forbidden to you, and I have come to you with a proof from your Lord. So fear Allah and obey me.
51. Truly! Allah is my Lord and your Lord, so worship Him (Alone). This is the Straight Path.
52. Then when Iesa (Jesus) came to know of their disbelief, he said: "Who will be my helpers in Allah’s Cause?" Al-Hawarioon (the disciples) said: "We are the helpers of Allah; we believe in Allah, and bear witness that we are Muslims (i.e. we submit to Allah)."
53. Our Lord! We believe in what You have sent down, and we follow the Messenger (Iesa (Jesus)); so write us down among those who bear witness (to the truth i.e. La ilaha ill-Allah - none has the right to be worshipped but Allah).
54. And they (disbelievers) plotted (to kill Iesa (Jesus) ), and Allah planned too. And Allah is the Best of the planners.
55. And (remember) when Allah said: "O Iesa (Jesus)! I will take you and raise you to Myself and clear you (of the forged statement that Iesa (Jesus) is Allahs son) of those who disbelieve, and I will make those who follow you (Monotheists, who worship none but Allah) superior to those who disbelieve (in the Oneness of Allah, or disbelieve in some of His Messengers, e.g. Muhammad, Iesa (Jesus),Moosa (Moses), etc., or in His Holy Books, e.g. the Taurat (Torah), the Injeel (Gospel), the Quran) till the Day of Resurrection. Then you will return to Me and I will judge between you in the matters in which you used to dispute."
56. "As to those who disbelieve, I will punish them with a severe torment in this world and in the Hereafter, and they will have no helpers."
57. And as for those who believe (in the Oneness of Allah) and do righteous good deeds, Allah will pay them their reward in full. And Allah does not like the Zalimoon (polytheists and wrong-doers).
Lastly, Allah says: That is because Allah has sent down the Book (the Qur’an) in truth. And verily, those who disputed as regards the Book are far away in opposition. (Al-Baqarah 2:176)