The anime movie doesn't really do the Berserker vs Shirou fight as much justice as it deserves.
A bit of background.
In the legend of Heracles, Hera had used her influence to force Heracles into murdering his family and his children. In his search for redemption he took on 12 labours and that is the legends that we know. In the Fate universe this is why he has such a fondness for Illya, He wants to protect children at all cost (let's ignore that Illya is an 18 year old homonculous), even as a berserker he surpases his own legend and retains that duty.
When Sakura absorbes Heracles and set's the black spirit loose on the escaping Shirou and Illya. Even then he does so to protect her. His eyes, nose, ears all removed by Sakura so he remains unaware. He has no senses, from his point of view he is still in that desperate fight with Saber to protect Illya.
From Shirou's point of view, he has abandoned the pursuit of justice he held so dear. He knows that Berserker will kill them both unless he can do something, Illya tells him to run and let her return to Berserker. But Shirou has sacrificed many lives to get this far and abandoned his ideals already so he knows he will never escape his crimes anyway.
He removes the wrapping that is protecting him from Archers arm, the flood of power surges into him with the force of a hurricane, there he see's it, a figure in red with his back turned. The figure knows there is no hope for Shirou and walks forward. Though as if to believe in Shirou's new ideals he asks "Can you keep up with me" in this hurricane like force. Shirou filled with determination replies "It's not me keeping up with you, CAN YOU KEEP UP WITH ME"
Shirou fights, he see's every weapon that Archer has ever forged, he needs a weapon that can kill the legendary Heracles, so he traces the stone sword that the berserker uses, retracing the 12 labours to build the foundation. Unlimited Blade Works can't be used as their ideals are too different. So to fill the sword with enough energy, chanting nine lives trigger off smashes all of his magic circuites to energise the sword. Shirou doesn't expect to survive so what does it matter if he breaks them now.
Then the two fight. Shirou holds his own but it's just a matter of time before he will falter. In an instant Heracles smashes down with all his might and to qoute the game "with the force that even the shockwave would shatter his head" but the attack doesn't come. Shirou looks up and see's the giant motionless, tears in his eyes crying. Heracles has realised what was happening and Shirou takes the opportunity to strike him. Heracles thanks Shirou for stopping him from repeating his legend and entrusts Illya to him.