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Having trailed 14-6 at the break to tries from Ballymena centres, Richard McKelvey and Kyle Moore, outhalf Luke Marshall with their own centre, Patrick Robinson kicking two penalties in between, MCB hit back at the start of the second half.
No 8, captain and later voted News Letter 'player of the match' Adam Macklin, went over twice from close range, with Robinson missing both touchline conversions. That had put the Belfast school 16-14 ahead, but Marshall then dropped a goal to swing the game back in Ballymena's favour.
But a Michael Allen try, converted by Robinson put 30-times winners MCB into a 23-17 lead. The drama continued with Moore going over in injury time, but there was to be agony for Ballymena as Marshall missed the difficult conversion which would have put them through.
The winners will meet the victors from the second semi-final between Ballyclare High and Regent House on Thursday at Ravenhill (2.30pm).