Movement verbs with the direction particle へ, transport with で, doing something with someone with と.
へ (read “e”) marks where you go/come/return. Used with 行きます, 来ます, 帰ります.
きょうとへ いきます。
I'm going to Kyoto.
へ marks the direction/destination of a movement verb. Just as the topic particle は is read “wa”, the particle へ is written へ but pronounced “e”.
で on a vehicle says how you travel: 電車で = “by train”.
でんしゃで かいしゃへ いきます。
I go to work by train.
で marks the means/method — here a vehicle. To say “on foot”, use 歩いて (no で).
と after a person means “(together) with”: 友達と = “with a friend”.
ともだちと にほんへ きました。
I came to Japan with a friend.
と links a companion to the action. To say “alone”, use 一人で.
いつ asks “when?”. Unlike clock times and dates, it never takes に.
いつ にほんへ きましたか。…さんがつにじゅうごにちに きました。
When did you come to Japan? … On March 25.
いつ stands where the time will stand in the answer. The answer may need に (３月２５日に), but いつ itself never takes it.