As the hero of Navarre rode past the house where he was born, he was trailing by eight and a half minutes the Danish rider who leads the Tour, and reached the Pamplona finish in an unfamiliar 19th place.
Any humiliation was eased by the crowds, the graffiti, and the banners that spread over seven mountain passes from France and into Spain. It was the toughest day of the toughest race, but agonisingly so for Indurain, the man of the people.
He is heading for Sunday's finale in Paris with a deficit of 15min, 36sec, unthinkable two weeks ago, and for many Spaniards unbelievable.
Messages of support flew from trees and houses and clung to hillocks: "You are unique...five is enough...Miguel the great...our man, our hero." The roads were almost white with paint from the amateur sign-writers of the Tour. Some signs were smeared into the sun-softened tar.
He was not alone in the doldrums. Riis showed no loss of power from Tuesday's winning drive to the summit of Hautacam, and the holder of the yellow jersey was the force behind the leading group of eight.
Yet before masses of Indurain fans, Riis could not hold the lively Swiss Laurent Dufaux, whose sprint took him clear of the Dane to an overdue victory in this 17th stage over 262 km from Argeles-Gazost, near Lourdes.
The combined pace of the leaders shook the weak links from the top standings, and future contenders were born on the longest day of this Tour.
After more than seven hours in the saddle under a grilling sun, the challenge of Abraham Olano, Tony Rominger and Yevgeny Berzin melted. Olano slid from second overall to ninth, more than 11 minutes behind Riis, and Rominger slipped from third to 10th, as they rode in with Indurain past cheering thousands to reach the finishing straight, with deafening chants of "Miguel, Miguel" for the final 400 metres.
He joined Riis on the podium, and the Dane raised Indurain's arm, a gracious gesture, and the crowd responded by singing Indurain's name, and the soulful eyes of their champion brimmed with tears.
"I am the leader today," Riis said. "But Miguel is and always will remain a great champion. I am sad for him but I am sure that he will be back. He understands that in the Tour no one can give 'presents'."
Dufaux, however, got his opportunity. He has worked hard to help his French team-mate, Richard Virenque, towards a hat-trick of red polka dot jerseys for the best mountain climber.
"This is a reward for all the efforts I have made for Richard," he said. "Riis was not going to let me win easily. He is incredibly strong and he wants to show who is the boss.
"It was a terrible day, and we were all tired but we worked well. Once the Indurain group closed to within three minutes of us, but we worked harder still to widen the gap."
Apart from Dufaux - who now replaces Tony Rominger and Alex Zulle as Switzerland's best hope - there is Riis's German team-mate Jan Ullrich. He is now the nearest to Riis by 3:59, and an Austrian challenger, Peter Luttenberger, has risen to fifth as the old Tour order changes.
Britain's Chris Boardman and many others lost more than 45 minutes during the stage. "I know it is not doing my Olympic prospects much good but I must get to the finish in Paris," he said.
As the leaders reached the bottom of the Col de Soudet, Basque separatists attempted to form a human blockade. The riders came to a stop, but a path was soon cleared by the gendarmerie, and the protesters returned to pushing leaflets and stickers through the windows of passing cars.
They have warned the Tour that it will not leave Spain unharmed, and today's stage from Pamplona to Hendaye in France will again be watched over by armed civil guards and police.
TOUR DE FRANCE DETAILS
STAGE 17 (Argeles-Gazost to Pamplona, 162.8 miles): 1 L Dufaux (Swit) Festina 7hr 7min 8sec; 2 B Riis (Den) Deutsche Telekom same time; 3 R Virenque (Fr) Festina +20sec; 4 J Ullrich (Ger) Deutsche Telekom; 5 L Leblanc (Fr) Polti; 6 P Ugrumov (Lat) Roslotto; 7 F Escartin (Sp) Kelme; 8 P Luttenberger (Aut) Carrera all same time; 9 M Lelli (It) SAECO +8:28; 10 P Savoldelli (It) Roslotto same time; 11 N Stephens (Aus) ONCE +8:30; 12 T Rominger (Swit) Mapei; 13 M Fernandez Gines (Sp) Mapei; 14 B Hamburger (Den) TVM; 15 G Guerini (It) Polti; 16 P Jonker (Aus) ONCE; 17 L Brochard (Fr) Festina; 18 M Bartoli (It) MG Technogym; 19 M Indurain (Sp) Banesto; 20 Alberto Elli (It) MG Technogym all same time. Selected: 106 C Boardman (GB) GAN +45:07.
Overall standings: 1 Riis 81:15:34; 2 Ullrich +3min 59sec; 3 Virenque +4:25; 4 Dufaux +5:52; 5 Luttenberger +6:19; 6 Escartin +7:23; 7 Ugrumov +7:48; 8 Leblanc +8:01; 9 Olano +11:12; 10 Rominger +11:24; 11 Indurain +15:36; 12 Hamburger +19:18; 13 L Piepoli (It) Refin +19:31; 14 F Gines +21:37; 15 U Bolts (Ger) Deutsche Telekom +23:05; 16 Brochard +31:32; 17 Jonker +33:03; 18 Elli +37:15; 19 Y Berzin (Russia) Gewiss +37:22; 20 V Ekimov (Russia) Rabobank +42:10. Selected: 41 Boardman +1hr 27min 33sec.
King of the Mountains: 1 Virenque 383pts; 2 Riis 274; 3 Dufaux 176; 4 Brochard 163; 5 Leblanc 158.
Points: 1 E Zabel (Ger) Deutsche Telekom 265; 2 F Moncassin (Fr) GAN 208; 3 F Baldato (It) MG Technogym 188; 4 D Abdoujaarov (Uzb) Refin 149; 5 Riis 12.Reuse content