They will contextualise your grades to an extent, but how do your other grades and the rest of the things on your application compare? If you have excellent leaving qualifications (A-Level, French Baccalaureate, IB, etc) and a strong PS and reference, then you may still have a chance, however it is, unfortunately, very unlikely that they will give you an offer or even an interview without a seriously compensating application. Oxford looks at your proportion of A* equivalents (now 8/9s) compared to your cohort, and if you have no A*s, you won't come across well in that metric.
Your best shot is to absolutely excel between now and when you apply, for example, with Olympiads, getting straight A*s at A-Level, getting relevant super-curriculars and having an explanation on your reference for your comparatively poor GCSEs. Another option to consider may be applying to Cambridge for a similar course (such as Chemical Engineering through Natural Sciences) as they do not focus on GCSEs as much and they have an Extenuating Circumstances Form separate from your reference, where you can explain your circumstances.
You will be against many people who have similar circumstances: lost teaching time, EFL etc. who have got excellent grades so it is an uphill battle, I'm afraid.