Alternate timeline (Journey to the Centre of the TARDIS)

In an alternate timeline, the Doctor's TARDIS was caught in a magnetic hobble-field from a space salvage ship, operated by the Van Baalen Bros. The TARDIS was successfully captured by the Van Baalen Bros., causing the TARDIS to leak the past and future. As such, several alternate timelines were created. (TV: Journey to the Centre of the TARDIS)

Original timeline
While teaching Clara Oswald how to fly the TARDIS as the ship had made it clear it didn't like her, the Eleventh Doctor lowered the TARDIS' shields, putting it into basic mode. Because of such, it was detectable to the Van Baalen Bros., who attempted to salvage it with a magno grab. The result of such severely damaged the TARDIS, causing an explosion. To save the Doctor and Clara, the TARDIS "wrapped her hands" around the heart of the blast, temporarily freezing it.

In the confusion, the Doctor made it out of the TARDIS, while Clara was lost inside. The Doctor soon met the Van Baalen brothers, who were unable to enter the TARDIS, taking the remote control for the magno-grab out of Gregor's pocket. He then cunningly lured them into the TARDIS, promising "the salvage of a lifetime". However, the Doctor forced the brothers, Gregor, Bram and Tricky, to help him find Clara by putting the TARDIS in lock-down and setting a non-existent self-destruct program, revealing the salvage he meant was not the ship but Clara.

Eventually, they found Clara in another echo room. The Doctor pulled her to safety and revealed the apparent self-destruct program had been a ruse. However, he found the engines had become unstable due to time leakage triggered by the incident, requiring a trip to the engine room to fix the problem.

While travelling through the Eye of Harmony, the quintet were trapped inside. They soon were burnt by the eye, transforming into molten time zombies. (TV: Journey to the Centre of the TARDIS)

Using the magno grab
In the next version of history, the time zombies the group had become leaked out into the past because of the TARDIS malfunctioning. This time, Gregor told Bram to dismantle the TARDIS console despite his protests. While doing so, his time zombie from the original timeline killed him. Clara was also chased around the TARDIS by her time zombie, incidentally finding a book about the history of the Last Great Time War, reading an extract from it, revealing the Doctor's name.

Upon retrieving Clara in this timeline and making their way to the Eye of Harmony, having been chased by the time zombies, the Doctor revealed the zombies were echoes of himself and the others, burnt by the Eye. Gregor and Tricky ended up turning into them, and the Doctor and Clara were forced to run away from them, ending up in a chasm. Believing they were going to die, the Doctor admitted that he knew her two previous incarnations and demanded to know what she really was. Clara didn't understand anything, leading the Doctor to deduce to himself there couldn't be a connection.

Realising the chasm wasn't really a chasm, but the TARDIS "snarling", the duo jumped from the chasm, ending up in the engine room. Finding it frozen, the Doctor eventually realised they had to use the magno grab to change time. They returned to the main control room, where Clara revealed she knew the Doctor's name. The Doctor used his sonic screwdriver to melt the words "BIG FRIENDLY BUTTON" onto the device, in the hope his past self would read them and use the button to stop the salvage. The Doctor then tossed the magno grab into the past through a leak in the room. (TV: Journey to the Centre of the TARDIS)

Burning Clara's hand
In the third alternate timeline, the events played out as they did in the second, except Clara picked up the magno-grab remote, burning the words "BIG FRIENDLY BUTTON" onto her hand. Eventually, the Doctor discovered the burnt imprint in the engine room, realising he would have to take the magno grab back to the point of the disaster himself to ensure his past self obtained it before the explosion. After he promised Clara that she wouldn't remember any of the events that had happened, the Doctor passed through a time rift to give the device to his past self. After instructing his past self to use the device, the future Doctor disappeared back through the rift. (TV: Journey to the Centre of the TARDIS)

Changing the past
Now having the magno-grab remote, the younger Doctor pressed the button, which shut down the Van Baalen Bros. magno-grab, allowing the TARDIS to dematerialise before it could suffer damage. (TV: Journey to the Centre of the TARDIS) The Doctor later displayed knowledge of all the alternate timelines. Clara also momentarily regained the knowledge, specifically about the Doctor confronting her about her identity when she was traveling through yet another alternate timeline where the TARDIS was damaged. (TV: The Name of the Doctor)

Despite the events occurring in the TARDIS, the altered timeline affected the relationship between the Van Baalen Bros. In this timeline, Gregor treated his little brother Tricky with more respect and their formerly damaged family photograph was intact. (TV: Journey to the Centre of the TARDIS)