Well, that was not supposed to happen. Chelsea's 29-match unbeaten home run in Europe is over after a performance that lacked drive, incision, leadership and any real sense of an attacking plan B. An excellent Basel team were deserved winners at Stamford Bridge after a display of great energy and no little craft.

But for José Mourinho there are some unexpectedly grave early-season questions after a week that has brought consecutive defeats, with the pre- and post-talk about the extreme youth of Mourinho's squad looking a little hollow.

The average age of Chelsea's team here was 28. Those are some hard-boiled eggs. Mourinho, at least, is still pushing back the boundaries. This is not just a sluggish start but the worst for any manager under Roman Abramovich. There were even boos at the end as Chelsea left the pitch. After the peculiar contortions of last season under Rafael Benítez it was all a bit like old times at Stamford Bridge – only, of course, without the victories in Europe.

If it is not time to panic just yet, the narrative of Mourinho's return has undoubtedly veered off into unexpected territory after a first home defeat in the Champions League group stages for 10 years. There are two immediate questions. Is this really the first knockings of what amounts to a crisis in the rarefied air of Stamford Bridge? And if it is, how well placed is Mourinho to fix it?

Certainly there are questions remaining about a squad blessed with wonderful, soft-shoed, creative resources but lacking a peak-condition, high-quality striker. At times this season, for all their promisingly intricate approach work, Chelsea have resembled a brilliantly armoured cavalryman riding into battle waving a baguette.

If they missed a sense of drive in the middle of the pitch, not to mention those familiar qualities of muscular leadership and even a little arrogance, they also lacked the kind player who can rescue a match when the wiles of that attacking midfield fail to carry the day. Among the many banners draped behind the Stamford Bridge goals is one devoted to Didier Drogba, the greatest signing of Mourinho MK1 and a player made for a night like this.

There was even something poignant in the identity of the scorer of Basel's winning goal. Marco Streller, a vast, gangling, entirely orthodox No9, reacted quickest at the near post to head Behram Safari's corner past Petr Cech and score the kind of seasoned centre-forward's goal that Chelsea have been notably lacking of late.

In the build-up to this match Mourinho had taken the most un-Mourinho-like course of pointing to his own team's deficiencies, rekindling an epic farmyard metaphor dating back to his departure from Chelsea eight years ago. If the intention was to lend his youthful midfield a little high-end underdog momentum, he will surely have had his thoughts on other kinds of weakness. Chelsea have an overload of creative midfielders. He does not need any more eggs or hens. What he lacks is something a little more predatory and sharp-beaked, which is why he tried so hard to sign Wayne Rooney this summer.

Here Samuel Eto'o started as lone striker ahead of a midfield trio of Oscar, in a central position, and Eden Hazard and Willian interchanging on the flanks. He played mainly with his back to goal, a little isolated from his team-mates, occasionally unfurling one of his favourite spiralling runs into space between the full-backs. Eto'o should be match fit – he has been playing matches – and he moved intelligently in the opening hour. But somehow he does not look quite there yet for all his eagerness in harrying the Basel centre-backs in a claustrophobic first half.

Chelsea's goal just before half-time was made by two crisp passes from David Luiz and Frank Lampard, Oscar finding space with a diagonal run and whipping the ball back into the corner across Yann Sommer. After this they created very little. Basel's equaliser was nicely put away by the waspish and inventive Mohamed Salah. Mourinho responded by bringing on Ba to make his Champions League debut. It never looked like being enough.

Whether Chelsea's manager can respond more decisively now remains to be seen. There will, of course, be wider issues teased into view by a couple of poor results and one bad performance: the debilitating effects of Chelsea's managerial promiscuity, the sense of a team constantly in transition, not to mention the manager's own suitability for what is an unfamiliar situation.

Mourinho has had bad results but he has never had a start to a season quite like this. If there has at times been a peculiar anti-swagger, a slightly jarring absence of outright, preening self-belief second time around at Stamford Bridge, perhaps Mourinho is aware of the different challenges facing him this time, the need to build from a position compromised by his failed pursuit of Rooney and with a squad with which he has already expressed his own dissatisfaction. It is perhaps not quite a crisis. But it is certainly new territory for Chelsea's manager. What he does next will, as ever, be fascinating.